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The structure of part of a DNA double helix
.Deoxyribonucleic acid (en-us-Deoxyribonucleic_acid.ogg /diˈɒksɪˈraɪboʊnuˈkliɪk ˈæsɪd/ ) (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses.^ In other embodiments, the kits comprise the conjugates described herein, with instructions for using the conjugate to detect affinity of anindividual's anti-ds DNA antibodies for the conjugate.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Proteins are fundamental components of all living cells and include many substances, such as enzymes, hormones, and antibodies, that are necessary for the proper functioning of an organism.

^ "During an organisms growth phase from embryo to adult some of the DNAs instructions remain inactive until the requisite level of maturity has been reached, at which point they are stimulated into action."

.The main role of DNA molecules is the long-term storage of information.^ DNA DNA is a molecule that encodes genetic information.
  • Understanding DNA 19 November 2009 18:56 UTC www.dnahelp.org [Source type: Academic]

^ DNA is a highly charged molecule, and can be view, to a first approximation, as a long polyelectrolyte with a large negative.
  • BC Online: 4A - Structure of DNA 19 January 2010 18:22 UTC employees.csbsju.edu [Source type: Academic]

^ Overview of Procedure DNA is the main carrier of genetic information in living organisms.
  • Automated DNA Sequencing 19 January 2010 18:22 UTC www.p2000.umich.edu [Source type: Academic]

.DNA is often compared to a set of blueprints or a recipe, or a code, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules.^ In other embodiments, the kits comprise the conjugates described herein, with instructions for using the conjugate to detect affinity of anindividual's anti-ds DNA antibodies for the conjugate.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Proteins are fundamental components of all living cells and include many substances, such as enzymes, hormones, and antibodies, that are necessary for the proper functioning of an organism.

^ A "double-stranded DNA epitope" or "dsDNA epitope" is any chemical moiety which exhibits specific binding to an anti-double-stranded DNA antibody and as such includes molecules which comprise such epitope(s).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

.The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.^ DNA information is carried by four bases.

^ In other embodiments, the kits comprise the conjugates described herein, with instructions for using the conjugate to detect affinity of anindividual's anti-ds DNA antibodies for the conjugate.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ It is further understood that a different polynucleotide (for example, in terms of size and/or sequence) other than the one that is to be, was, or will be used in treatment, as long as both polynucleotides exhibit equivalent (or convertible)binding affinities to anti-ds DNA antibodies from an individual.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

.Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds.^ DNA is the long two stranded chain.

^ A few contacts with the DNA backbone are made by two helices.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

These two strands run in opposite directions to each other and are therefore anti-parallel. .Attached to each sugar is one of four types of molecules called bases.^ There are four types of bases.
  • Gene definition - Medical Dictionary definitions of popular medical terms easily defined on MedTerms 16 January 2010 1:27 UTC www.medterms.com [Source type: Academic]

^ A nucleoside is one of the four DNA bases covalently attached to the C1' position of a sugar.

^ And, again, the bases are attached to the first carbon of the sugar molecule.

.It is the sequence of these four bases along the backbone that encodes information.^ The sequence of these four bases encodes the information and is the genetic code of all of us ( more information ...
  • Home - DNA rainbow 19 January 2010 18:22 UTC www.dna-rainbow.org [Source type: FILTERED WITH BAYES]

^ DNA information is carried by four bases.

^ Scientists use these base sequences to locate the position of genes on chromosomes and to construct a map of the entire human genome.
  • DNA Molecule - Picture - ninemsn Encarta 16 October 2009 6:06 UTC au.encarta.msn.com [Source type: Academic]

.This information is read using the genetic code, which specifies the sequence of the amino acids within proteins.^ Transcribe the DNA code to RNA code, then translate the RNA code to an amino acid sequence.
  • DNA Structure and Function 19 January 2010 18:22 UTC biology.clc.uc.edu [Source type: FILTERED WITH BAYES]

^ Useful when sequence information is limited .
  • Ambion, Inc. - Probe Labeling Chart 20 September 2009 12:012 UTC www.ambion.com [Source type: Reference]

^ DNA contains the genetic codes to make RNA and the RNA in turn then contains the codes for the primary sequence of amino acids to make proteins.

.The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.^ Transcribe the DNA code to RNA code, then translate the RNA code to an amino acid sequence.
  • DNA Structure and Function 19 January 2010 18:22 UTC biology.clc.uc.edu [Source type: FILTERED WITH BAYES]

^ This process is called DNA fingerprinting.

^ Stretches of DNA (or stretches of chromosomes) code for genes.

.Within cells, DNA is organized into long structures called chromosomes.^ The structure of the zipper-type proteins may be split into two parts: the dimerization and DNA-binding regions.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ But unknowns to you there are things called parasitic genes that reproduce by inserting copies of themselves into new locations in the chromosomes.

^ Genome analysis will not only facilitate identification of such proteins, but will allow us to determine functionally important target sites on the DNA and, in combination with structural data, how higher-order oligomers are formed within the cell.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.These chromosomes are duplicated before cells divide, in a process called DNA replication.^ This process is called DNA fingerprinting.

^ All of the DNA in a cell is found in individual pieces, called chromosomes.
  • DNA - an introduction and overview 19 January 2010 18:22 UTC www.eurekascience.com [Source type: FILTERED WITH BAYES]

^ How many times is a cell's DNA replicated before it divides?

.Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts.^ In some embodiments, the ds DNA epitope is a polynucleotide, such as 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO:1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[1] In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. .Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.^ DNA is associated with proteins: histones and non histone proteins, to form the chromatin.

^ In simple terms, DNA controls the production of proteins within the cell.
  • DNA - The Double Helix 19 January 2010 18:22 UTC biologycorner.com [Source type: Academic]

^ Dataset of protein-DNA complex structures .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

Contents

Properties

Chemical structure of DNA. Hydrogen bonds shown as dotted lines.
DNA is a long polymer made from repeating units called nucleotides.[2][3][4] .The DNA chain is 22 to 26 Ångströms wide (2.2 to 2.6 nanometres), and one nucleotide unit is 3.3 Å (0.33 nm) long.^ The final concentration of the ct DNA preparation was determined spectrophotometrically assuming an extinction coefficient of 33 .mu.g per 1 OD unit at 260 nM. .
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[5] .Although each individual repeating unit is very small, DNA polymers can be very large molecules containing millions of nucleotides.^ Accordingly, the invention includes kits containing (i.e.,comprising) one or more dsDNA epitopes, preferably polynucleotides (preferably, double stranded (ds) DNA molecules) comprising an epitope which binds to an anti-ds DNA antibody from an individual (and the epitope-containing polynucleotide binds to ananti-ds DNA antibody from an individual).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The amino-terminal domain contains five helices and the large carboxy-terminal domain is primary a helical with a small ß sheet packing against a nine-helix domain (Figure 4e .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ This group, which only contains the TATA box-binding protein family, is characterized by the use a large ß-sheet structures to bind the DNA (Figure 5 ).
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

For instance, the largest human chromosome, chromosome number 1, is approximately 220 million base pairs long.[6]
In living organisms, DNA does not usually exist as a single molecule, but instead as a pair of molecules that are held tightly together.[7][8] .These two long strands entwine like vines, in the shape of a double helix.^ Two pairs of conserved histidine and cysteine residues in the a helix and second ß strand coordinate a single zinc ion.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The DNA-binding region of the E2 protein (Figure 4a ) is about 85 residues long and consists of four ß strands and two interstrand a helices.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The structure of the finger is characterized by a short two-stranded antiparallel ß sheet followed by an a helix (Figure 2a ).
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.The nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand in the helix.^ Line 4 : Each DNA molecule is a long two stranded chain.

^ The nucleotides joined together to form a chain.

^ In a double helix, the direction of the nucleotides in one strand is opposite to that in the other strand.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.A base linked to a sugar is called a nucleoside and a base linked to a sugar and one or more phosphate groups is called a nucleotide.^ The complexes were defined as any structure containing one or more protein chains and at least one double-stranded DNA of more than four base-pairs (bp) in length.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The prokaryotic enzymes in the group (for example, Fok I endonuclease, 1fok) which function as monomers possess more than one motif in a single subunit.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

If multiple nucleotides are linked together, as in DNA, this polymer is called a polynucleotide.[9]
.The backbone of the DNA strand is made from alternating phosphate and sugar residues.^ What sugar is DNA made of?
  • WikiAnswers - What is DNA made of 19 January 2010 18:22 UTC wiki.answers.com [Source type: General]

^ The sugars and phosphates in the "backbone" of a DNA strand are held together by ________.
  • Biology: Life on Earth 6E Chapter 9 -- Multiple Choice 20 September 2009 11:58 UTC cwx.prenhall.com [Source type: Academic]

^ The strands of the DNA molecule are made-up of two molecules, the sugar and the phosphate molecules.
  • Dynamic model of the DNA molecule - US Patent 6036497 Description 16 October 2009 6:06 UTC www.patentstorm.us [Source type: Reference]

[10] The sugar in DNA is 2-deoxyribose, which is a pentose (five-carbon) sugar. .The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings.^ The nucleotides joined together to form a chain.

^ A backbone or scaffold is provided by groups of atoms that form phosphate and deoxyribose.

^ The deoxyribose sugars are joined at both the 3'-hydroxyl and 5'-hydroxyl groups to phosphate groups in ester links, also known as "phosphodiester" bonds.
  • Introduction to DNA Structure 20 September 2009 11:58 UTC www.blc.arizona.edu [Source type: Reference]

.These asymmetric bonds mean a strand of DNA has a direction.^ The DNA strands are assembled in the 5 to 3 direction and,.
  • Definition: DNA from Online Medical Dictionary 20 September 2009 11:58 UTC dvfreelancer.com [Source type: FILTERED WITH BAYES]

^ Because these bonds are asymmetric, a strand of DNA has a 'direction'.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The first major step for the DNA Replication to take place is the breaking of hydrogen bonds between bases of the two antiparallel strands.

.In a double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand: the strands are antiparallel.^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

.The asymmetric ends of DNA strands are called the 5′ (five prime) and 3′ (three prime) ends, with the 5' end having a terminal phosphate group and the 3' end a terminal hydroxyl group.^ The proteins consist of an incomplete five-stranded ß-barrel capped by an a helix abutting three ß strands (Figure 6e ).
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Each subunit consists of a seven-strand antiparallel ß barrel; one opening of this barrel forms a dimer interface with the equivalent segment of the other subunit while the other end points towards the DNA. .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The zinc-coordinating motif is found in the DNA-binding domain and is characterized by two antiparallel a helices capped by loops at their amino-terminal ends.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

One major difference between DNA and RNA is the sugar, with the 2-deoxyribose in DNA being replaced by the alternative pentose sugar ribose in RNA.[8]
.
A section of DNA. The bases lie horizontally between the two spiraling strands.
^ Detection and measurement of indicators of efficacy are generally based on measurement of anti-double-stranded DNA antibody and/or clinical symptoms associated with SLE, which are known in the art.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[11] Animated version at File:DNA orbit animated.gif.
.The DNA double helix is stabilized by hydrogen bonds between the bases attached to the two strands.^ Within the DNA double helix, A forms 2 hydrogen bonds with T on the opposite strand, and G forms 3 hyrdorgen bonds with C on the opposite strand.

^ Two and three hydrogen bonds are formed in A - T and G - C base pairs, respectively.
  • An Introduction to DNA Structure 20 November 2009 8:55 UTC www.callutheran.edu [Source type: Academic]

^ What is the DNA double helix?
  • genome.gov | Deoxyribonucleic Acid (DNA) 19 January 2010 18:22 UTC www.genome.gov [Source type: Academic]
  • DNA - WikiGenetics 19 January 2010 18:22 UTC www.wikigenetics.org [Source type: Academic]

.The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T).^ Four different nucleotide bases occur in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T).

^ This is a molecular kit to make open models of the 4 individual bases present in DNA, Adenine, Cytosine, Guanine and Thymine.

^ One of the biggest puzzles was that although the proportion of these bases varied from one DNA to another, it was always found that the number of A = T, and G = C. .

These four bases are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate.
.These bases are classified into two types; adenine and guanine are fused five- and six-membered heterocyclic compounds called purines, while cytosine and thymine are six-membered rings called pyrimidines.^ The base, however, can be one of four bases: Adenine, Thymine, Guanine, and Cytosine.
  • Dynamic model of the DNA molecule - US Patent 6036497 Description 16 October 2009 6:06 UTC www.patentstorm.us [Source type: Reference]

^ Guanine is so, adenine la and cytosine do.
  • DNA Makes Sweet Music! - CBS News 19 January 2010 18:22 UTC www.cbsnews.com [Source type: General]

^ Adenine bonds to thymine and guanine bonds to cytosine.

[8] .A fifth pyrimidine base, called uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring.^ A major difference between DNA and RNA is that DNA contains thymine, but not uracil, while RNA contains uracil but not thymine.

^ BASE PAIRING RULE For RNA: ( Remember that uracil replaces thymine) .

^ Pyrimidines - have a single ring on their nitrogenous base: .

.Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine.^ Cytosine (C) - found in both DNA and RNA .

^ Nucleotide : A subunit of DNA or RNA consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate molecule, and a sugar molecule (deoxyribose in DNA and ribose in RNA).

^ A fifth pyrimidine base, uracil (U), replaces thymine in RNA. Uracil is normally only found in DNA as a breakdown product of cytosine, but bacterial viruses contain uracil in their DNA. [22] In contrast, following synthesis of certain RNA molecules, many uracils are converted to thymines.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.In addition to RNA and DNA, a large number of artificial nucleic acid analogues have also been created to study the proprieties of nucleic acids, or for use in biotechnology.^ The terms "polynucleotide" and "nucleic acid", used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[12]

Grooves

.Twin helical strands form the DNA backbone.^ Each subunit consists of a seven-strand antiparallel ß barrel; one opening of this barrel forms a dimer interface with the equivalent segment of the other subunit while the other end points towards the DNA. .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The MetJ repressor binds DNA as a dimer (Figure 6a ), each subunit comprising a helical bundle and a single ß strand; the strands from each subunit form the antiparallel sheet for DNA-binding (colored red).
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The IRF DNA-binding region has an a/ß architecture consisting of a cluster of three a helices flanked on one side by a mixed four-stranded ß sheet (Figure 1m ).
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.Another double helix may be found by tracing the spaces, or grooves, between the strands.^ Fingers bind adjacent 3 bp subsites by inserting the a helix in the major groove, and the recognition pattern between the helix and DNA is well characterized.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Conserved UDG residues in loop regions contact the DNA, with the loop between sheet 4 and helix 8 inserting into the DNA minor groove.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The amino-terminal arm and second a helix from D1 bind in the major groove and a loop preceding this recognition helix is found in the minor groove.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.These voids are adjacent to the base pairs and may provide a binding site.^ In other embodiments, valency platforms may be used which, when conjugated, provide an average valency (i.e., these platforms are not precisely chemically defined in terms of their valency).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Multiple iterations of these oligomers may be ligated in tandem to provide for multicopy replication.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ These polynucleotides may be designed to have appropriate termini for ligation into specificrestriction sites.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

As the strands are not directly opposite each other, the grooves are unequally sized. .One groove, the major groove, is 22 Å wide and the other, the minor groove, is 12 Å wide.^ Jointly the domains form a clamp around the DNA, inserting a helices into both the major and minor grooves [ 45 ].
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The recognition helix of the HTH motif is bound in the major groove and other a helices make DNA backbone contacts.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Like those of leucine zippers, the dimerization helices interact with each other in a coiled-coil arrangement and the DNA-binding helices are inserted into the DNA major groove.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[13] .The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove.^ It presents a major groove and a minor groove.

^ II.2.2 Major groove and minor groove .

^ Most of these interactions occur in the major groove, where the bases are most accessible.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.^ While the interaction on the major groove side is distinct for the direction of the base pair (e.g.
  • Drug-DNA interaction 20 November 2009 8:55 UTC www.whatislife.com [Source type: Academic]

^ The major groove is the site where most protein-DNA interactions occur.
  • DNA and RNA structures 19 January 2010 18:22 UTC www.whatislife.com [Source type: Academic]

^ Double-stranded DNA Viruses.
  • Double-stranded DNA Viruses 19 January 2010 8:50 UTC tolweb.org [Source type: FILTERED WITH BAYES]

[14] .This situation varies in unusual conformations of DNA within the cell (see below), but the major and minor grooves are always named to reflect the differences in size that would be seen if the DNA is twisted back into the ordinary B form.^ While achieving a close fit between the a helix and major groove, there is enough flexibility to allow both the protein and DNA to adopt distinct conformations, resulting in multispecific complementarity.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ In contrast to the two families above, the integration host factor forces an enormous distortion in the DNA by inserting a ß hairpin from each subunit in the minor groove (red in Figure 6c ).
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ In contrast to many protein families, the a helix binds base and backbone groups from the DNA minor groove [ 51 ].
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

Base pairing

.Each type of base on one strand forms a bond with just one type of base on the other strand.^ Each type of base on one strand of DNA forms a bond with just one type of base on the other strand, called 'complementary base pairing '.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ "On any given day, any one of the four could have beaten the others; it was just a question of to whom the day would go that particular day."
  • Top Chef | Bravo TV Official Site 16 January 2010 1:27 UTC www.bravotv.com [Source type: FILTERED WITH BAYES]

^ The recognition sequence is often a six base pair palindromic sequence (the top DNA strand from 5' to 3' is the same as the bottom DNA strand from 5' to 3'), but others recognize four or even eight base pair sequences.
  • Restriction Enzyme Analysis of DNA-Student Handout 16 October 2009 6:06 UTC biotech.biology.arizona.edu [Source type: FILTERED WITH BAYES]

.This is called complementary base pairing.^ This pairing is called complementary base pairing .

^ These pairings also referred as complementary base pairs.
  • science tips 16 October 2009 6:06 UTC rpdp.net [Source type: Academic]

^ A pairs with T and C pairs with G to form units called base pairs .

.Here, purines form hydrogen bonds to pyrimidines, with A bonding only to T, and C bonding only to G. This arrangement of two nucleotides binding together across the double helix is called a base pair.^ Note that the C-G pair has three hydrogen bonds while the A-T pair has only two, which keeps them from pairing wrong.
  • DNA Structure and Function 19 January 2010 18:22 UTC biology.clc.uc.edu [Source type: FILTERED WITH BAYES]

^ The nucleotides joined together to form a chain.

^ The double helix is held together by hydrogen bonds between the bases attached to the two strands.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily.^ Hydrogen bonds can be broken and rejoined quite easily, so the two strands of DNA in a double helix can be pulled apart like a zipper, either by mechanical force or by high temperatures.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ High ionic strength, however, reduces non covalent interaction mediated by hydrogen bonds and electrostatic interactions.
  • Drug-DNA interaction 20 November 2009 8:55 UTC www.whatislife.com [Source type: Academic]

^ As your students correctly join the nucleotides, they will "feel" hydrogen bonding.

.The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force or high temperature.^ Hydrogen bonds can be broken and rejoined quite easily, so the two strands of DNA in a double helix can be pulled apart like a zipper, either by mechanical force or by high temperatures.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA double helix 7-038 .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

^ What is the DNA double helix?
  • genome.gov | Deoxyribonucleic Acid (DNA) 19 January 2010 18:22 UTC www.genome.gov [Source type: Academic]
  • DNA - WikiGenetics 19 January 2010 18:22 UTC www.wikigenetics.org [Source type: Academic]

[15] .As a result of this complementarity, all the information in the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in DNA replication.^ DNA double helix 7-038 .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

^ What is the DNA double helix?
  • genome.gov | Deoxyribonucleic Acid (DNA) 19 January 2010 18:22 UTC www.genome.gov [Source type: Academic]
  • DNA - WikiGenetics 19 January 2010 18:22 UTC www.wikigenetics.org [Source type: Academic]

^ The double-stranded structure of DNA provides a simple mechanism for this replication.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.Indeed, this reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms.^ The reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ That it had a specific base pairing.
  • DNA double helix Watson Crick Wilkins Franklin 20 September 2009 11:58 UTC www.ba-education.com [Source type: FILTERED WITH BAYES]

^ These pairings also referred as complementary base pairs.
  • science tips 16 October 2009 6:06 UTC rpdp.net [Source type: Academic]

[3]
GC DNA base pair.svg
AT DNA base pair.svg
.Top, a GC base pair with three hydrogen bonds.^ Also G-C pairs form three hydrogen bonds, whereas A-T pairs have only two.

^ The bonds between G-C base pairs and A-T base pairs are called, hydrogen bonds.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

^ II.2.1 Hydrogen bounds: bases pairing .

.Bottom, an AT base pair with two hydrogen bonds.^ The bonds between G-C base pairs and A-T base pairs are called, hydrogen bonds.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

^ Complementary base pairs (e.g., adenine and thymine) that are joined by hydrogen bonds .
  • Biology: Life on Earth 6E Chapter 9 -- Multiple Choice 20 September 2009 11:58 UTC cwx.prenhall.com [Source type: Academic]

^ Also G-C pairs form three hydrogen bonds, whereas A-T pairs have only two.

Non-covalent hydrogen bonds between the pairs are shown as dashed lines.
.The two types of base pairs form different numbers of hydrogen bonds, AT forming two hydrogen bonds, and GC forming three hydrogen bonds (see figures, left).^ Note that the C-G pair has three hydrogen bonds while the A-T pair has only two, which keeps them from pairing wrong.
  • DNA Structure and Function 19 January 2010 18:22 UTC biology.clc.uc.edu [Source type: FILTERED WITH BAYES]

^ Bp : See base pair.

^ The bonds between G-C base pairs and A-T base pairs are called, hydrogen bonds.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

.DNA with high GC-content is more stable than DNA with low GC-content, but contrary to popular belief, this is not due to the extra hydrogen bond of a GC base pair but rather the contribution of stacking interactions (hydrogen bonding merely provides specificity of the pairing, not stability).^ Patients receiving this amount of conjugate, who had an initial K.sub.D' of less than about 0.8, displayed more than about two-fold lower hospitalizations due to this disorder.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ An antibody "specifically binds" to a target if it binds with greater affinity,avidity, more readily, and/or with greater duration than it binds to other substances.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Both proteins approach the minor groove, and the DNA-recognition regions reach around the side of the DNA to contact bases in the major groove using a pair of loops.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[16] .As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determine the strength of the association between the two strands of DNA. Long DNA helices with a high GC content have stronger-interacting strands, while short helices with high AT content have weaker-interacting strands.^ Line 4 : Each DNA molecule is a long two stranded chain.

^ Dynamics of the B-A transition of DNA double helices.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

^ With each of the 6 corners there are then associated two strands of DNA., which makes 12.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

[17] .In biology, parts of the DNA double helix that need to separate easily, such as the TATAAT Pribnow box in some promoters, tend to have a high AT content, making the strands easier to pull apart.^ The method of claim 2, wherein said double stranded DNA consists of the sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ As clearly indicated in the definition of "antibody" provided herein, a "anti-double-stranded DNA antibody" encompasses any fragment(s) that exhibits this requisitefunctional (i.e., specific binding to dsDNA) property, such as fragments that contain the variable region, such as Fab fragments.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The treatment entails administration of a conjugate comprising a non-immunogenic valency platform molecule and at least two double stranded DNA epitopes, such as DNA molecules, which bind to anti-DNA antibodies from the patient.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[18] In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their melting temperature (also called Tm value). .When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules.^ The strands of the DNA molecule are made-up of two molecules, the sugar and the phosphate molecules.
  • Dynamic model of the DNA molecule - US Patent 6036497 Description 16 October 2009 6:06 UTC www.patentstorm.us [Source type: Reference]

^ Figure 1: The DNA molecule showing base pairing.
  • science tips 16 October 2009 6:06 UTC rpdp.net [Source type: Academic]

^ DNA - double helix .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

.These single-stranded DNA molecules have no single common shape, but some conformations are more stable than others.^ These are important times; more so than any other time in history.
  • DNA Activation Music - DNA Recoding - DNA Restranding - Activate Your DNA through Sound 19 January 2010 8:50 UTC www.activateyourdna.com [Source type: General]

^ Single-stranded DNA and repair of mutations .
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

^ These molecules have no single shape, but some conformations are more stable than others.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[19]

Sense and antisense

.A DNA sequence is called "sense" if its sequence is the same as that of a messenger RNA copy that is translated into protein.^ DNA is copied into RNA by RNA polymerases .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ RNA is used in translation when the mRNA is "translated" into a protein.
  • The DNA double helix must unwind and separate into two strands so that one strand can assemble the proper 20 September 2009 11:58 UTC askville.amazon.com [Source type: General]

^ Translation: DNA to mRNA to Protein .
  • DNA Transcription | Learn Science at Scitable 19 January 2010 18:22 UTC www.nature.com [Source type: Academic]

[20] .The sequence on the opposite strand is called the "antisense" sequence.^ The sequence on the opposite strand is complementary to the sense sequence and is called the "antisense" sequence.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Some viruses blur the distinction between sense and antisense, because certain sequences of their genomes do double duty, encoding one protein when read 5' to 3' along one strand, and a second protein when read in the opposite direction along the other strand.
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

^ A set of two bonded nucleotides on opposite strands of DNA. There are two possible base pairs: C-G and A-T. These letters are used as shorthand for the sequences of fragments of DNA e.g.

Both sense and antisense sequences can exist on different parts of the same strand of DNA (i.e. both strands contain both sense and antisense sequences). In both prokaryotes and eukaryotes, antisense RNA sequences are produced, but the functions of these RNAs are not entirely clear.[21] .One proposal is that antisense RNAs are involved in regulating gene expression through RNA-RNA base pairing.^ Beta proteins are involved in gene expression regulation.

^ Regulation of gene expression .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ A gene has about one thousand to several million base pairs.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

[22]
.A few DNA sequences in prokaryotes and eukaryotes, and more in plasmids and viruses, blur the distinction between sense and antisense strands by having overlapping genes.^ The method of claim 2, wherein said double stranded DNA consists of the sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Preferably, the dsDNA epitopesare polynucleotides, said polynucleotide preferably comprising, consisting essentially of or consisting of the double stranded DNA sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The method of claim 10, wherein said double stranded DNA consists of the sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[23] .In these cases, some DNA sequences do double duty, encoding one protein when read along one strand, and a second protein when read in the opposite direction along the other strand.^ The DNA strands are assembled in the 5 to 3 direction and,.
  • Definition: DNA from Online Medical Dictionary 20 September 2009 11:58 UTC dvfreelancer.com [Source type: FILTERED WITH BAYES]

^ In a double helix, the direction of the nucleotides in one strand is opposite to that in the other strand.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Some viruses blur the distinction between sense and antisense, because certain sequences of their genomes do double duty, encoding one protein when read 5' to 3' along one strand, and a second protein when read in the opposite direction along the other strand.
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

In bacteria, this overlap may be involved in the regulation of gene transcription,[24] while in viruses, overlapping genes increase the amount of information that can be encoded within the small viral genome.[25]

Supercoiling

DNA can be twisted like a rope in a process called DNA supercoiling. .With DNA in its "relaxed" state, a strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted the strands become more tightly or more loosely wound.^ In its "relaxed" state, a DNA strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted, the strands become more tightly or more loosely wound.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA double stranded state is actually its "resting state".

^ The double helix is itself twisted.

[26] .If the DNA is twisted in the direction of the helix, this is positive supercoiling, and the bases are held more tightly together.^ If the DNA is twisted in the direction of the helix (positive supercoiling), and the bases are held more tightly together.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The two strands of a DNA double helix are held together by ________.

^ Each strand of the DNA molecule is held together at its base by a weak bond.
  • DNA 101 19 January 2010 18:22 UTC blairdna.com [Source type: Academic]

.If they are twisted in the opposite direction, this is negative supercoiling, and the bases come apart more easily.^ If they are twisted in the opposite direction (negative supercoiling) the bases come apart more easily.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The conformation of a DNA molecule depends on its sequence, the amount and direction of supercoiling, chemical modifications of the bases, and also solution conditions, such as the concentration of metal ions.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ A DNA segment with excess or insufficient helical twisting is referred to, respectively, as positively or negatively "supercoiled".
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

In nature, most DNA has slight negative supercoiling that is introduced by enzymes called topoisomerases.[27] .These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as transcription and DNA replication.^ Proofreading corrects errors made during the DNA replication process.

^ DNA during replication.

^ DNA can be 'twisted' in a process called DNA supercoiling .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[28]
From left to right, the structures of A, B and Z DNA

Alternate DNA structures

.DNA exists in many possible conformations that include A-DNA, B-DNA, and Z-DNA forms, although, only B-DNA and Z-DNA have been directly observed in functional organisms.^ Preferably, the polynucleotide is DNA. As used herein, "DNA" includes not only bases A, T, C, and G, but also includes any of their analogs or modified forms of these bases, such as methylated nucleotides, internucleotide modifications such asuncharged linkages and thioates, use of sugar analogs, and modified and/or alternative backbone structures, such as polyamides.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[10] The conformation that DNA adopts depends on the hydration level, DNA sequence, the amount and direction of supercoiling, chemical modifications of the bases, the type and concentration of metal ions, as well as the presence of polyamines in solution.[29]
.The first published reports of A-DNA X-ray diffraction patterns— and also B-DNA used analyses based on Patterson transforms that provided only a limited amount of structural information for oriented fibers of DNA.[30][31] An alternate analysis was then proposed by Wilkins et al., in 1953, for the in vivo B-DNA X-ray diffraction/scattering patterns of highly hydrated DNA fibers in terms of squares of Bessel functions.^ The above analysis, and that further described in Sem et al.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The term "circulating anti-double-stranded DNA antibody", as used herein, intends an anti-double-stranded DNA antibody which is not bound to a double-stranded DNA epitope on and/or in a biological sample, i.e., free antibody.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The invention thus provides screening based on any of a number of dsDNA epitopes contemplated for use in treatment.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[32] .In the same journal, Watson and Crick presented their molecular modeling analysis of the DNA X-ray diffraction patterns to suggest that the structure was a double-helix.^ It should be understood that it is not intended that the invention be limited by this belief and that theduplexes may, upon more conclusive analysis assume Z-DNA and/or A-DNA type helical structures.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[7]
.Although the `B-DNA form' is most common under the conditions found in cells,[33] it is not a well-defined conformation but a family of related DNA conformations[34] that occur at the high hydration levels present in living cells.^ Transformants are identified by standard markers and are grown under conditions that favor DNA replication.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

Their corresponding X-ray diffraction and scattering patterns are characteristic of molecular paracrystals with a significant degree of disorder.[35][36]
Compared to B-DNA, the A-DNA form is a wider right-handed spiral, with a shallow, wide minor groove and a narrower, deeper major groove. .The A form occurs under non-physiological conditions in partially dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes.^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ In addition, a double-strandedpolynucleotide can be obtained from the single stranded polynucleotide product of chemical synthesis either by synthesizing the complementary strand and annealing the strands under appropriate conditions, or by synthesizing the complementary strand denovo using a DNA polymerase with an appropriate primer.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The polynucleotides may be isolated from the other DNA of the cell/microorganism by treatment with restriction enzymes andconventional size fractionation (e.g., agarose gel, Sephadex.TM. column).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[37][38] Segments of DNA where the bases have been chemically modified by methylation may undergo a larger change in conformation and adopt the Z form. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form.[39] .These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in the regulation of transcription.^ Dataset of protein-DNA complex structures .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ DNA-binding proteins .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA binding proteins .

[40]
DNA quadruplex formed by telomere repeats. .The looped conformation of the DNA backbone is very different from the typical DNA helix.^ The backbone of thepolynucleotide can comprise sugars and phosphate groups (as may typically be found in RNA or DNA), or modified or substituted sugar or phosphate groups.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[41]

Quadruplex structures

.At the ends of the linear chromosomes are specialized regions of DNA called telomeres.^ DNA is linear and read from start to end.
  • DNA seen through the eyes of a coder 19 January 2010 18:22 UTC ds9a.nl [Source type: FILTERED WITH BAYES]

^ In its packaged form, DNA is called a chromosome .

^ At the ends of the linear chromosomes, specialized regions called telomeres allow the cell to replicate chromosome ends using the enzyme telomerase .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.The main function of these regions is to allow the cell to replicate chromosome ends using the enzyme telomerase, as the enzymes that normally replicate DNA cannot copy the extreme 3′ ends of chromosomes.^ The polynucleotides may be isolated from the other DNA of the cell/microorganism by treatment with restriction enzymes andconventional size fractionation (e.g., agarose gel, Sephadex.TM. column).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[42] These specialized chromosome caps also help protect the DNA ends, and stop the DNA repair systems in the cell from treating them as damage to be corrected.[43] .In human cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence.^ The method of claim 2, wherein said double stranded DNA consists of the sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The method of claim 1, wherein said polynucleotides comprise single stranded sequences.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Alternatively, pairs of complementary single-stranded polynucleotide chains up to about 70 bases in length are readily prepared using commercially available DNA synthesizers and then annealed to form duplexes by conventional procedures.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[44]
.These guanine-rich sequences may stabilize chromosome ends by forming structures of stacked sets of four-base units, rather than the usual base pairs found in other DNA molecules.^ One of the four base molecules present in DNA. .

^ Similar DNA structures may be produced by DNA with different nucleotide sequences.
  • Insertion site preferences of the P transposable element in Drosophila melanogaster 20 November 2009 8:55 UTC www.pubmedcentral.nih.gov [Source type: Academic]

^ The structure of DNA overstretched from the 5'5' ends differs from the structure of DNA overstretched from the 3'3' ends.
  • PDBsum entry: 3cmv 20 September 2009 12:012 UTC www.ebi.ac.uk [Source type: Academic]
  • PDBsum entry: 3cmt 20 September 2009 12:012 UTC www.ebi.ac.uk [Source type: Academic]

.Here, four guanine bases form a flat plate and these flat four-base units then stack on top of each other, to form a stable G-quadruplex structure.^ Preferably, the polynucleotide is DNA. As used herein, "DNA" includes not only bases A, T, C, and G, but also includes any of their analogs or modified forms of these bases, such as methylated nucleotides, internucleotide modifications such asuncharged linkages and thioates, use of sugar analogs, and modified and/or alternative backbone structures, such as polyamides.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[45] These structures are stabilized by hydrogen bonding between the edges of the bases and chelation of a metal ion in the centre of each four-base unit.[46] .Other structures can also be formed, with the central set of four bases coming from either a single strand folded around the bases, or several different parallel strands, each contributing one base to the central structure.^ Other structures can also be formed, and the central set of four bases can come from either one folded strand, or several different parallel strands, each contributing one base to the central structure.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Definition: The basic structural unit of DNA. Context: Each strand of a DNA molecule is a linear arrangement of nucleotides, which are each composed of one sugar, one phosphate, and one nitrogenous base.

^ In 1953, James Watson and Francis Crick determined that the structure of DNA is a double-helix polymer, a spiral consisting of two DNA strands wound around each other.
  • DNA (chemical compound) -- Britannica Online Encyclopedia 19 January 2010 18:22 UTC www.britannica.com [Source type: Academic]

.In addition to these stacked structures, telomeres also form large loop structures called telomere loops, or T-loops.^ Lymph node A structure the size of a bean that contains large numbers of lymphocytes and is connected to other lymph nodes by small channels called lymphatics.
  • Leukemia & Lymphoma Society - Disease Page Definitions 16 January 2010 1:27 UTC www.leukemia-lymphoma.org [Source type: Academic]

^ These proteins seem to stabilize single-stranded DNA and protect it from forming stem loops or being degraded by nucleases .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The presence in Mfd of the highly conserved TRG motif forming the helical hairpin and adjacent loop structures in RecG suggests that these two enzymes may have very similar translocation motors derived from a common ancestor.
  • A model for dsDNA translocation revealed by a structural motif common to RecG and Mfd proteins : Article : The EMBO Journal 20 September 2009 12:012 UTC www.nature.com [Source type: Academic]

.Here, the single-stranded DNA curls around in a long circle stabilized by telomere-binding proteins.^ Single-stranded DNA and repair of mutations .
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

^ DNA-binding proteins .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA binding proteins .

[47] .At the very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands.^ Single-stranded DNA and repair of mutations .
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

^ Two strands of DNA are held together in the shape of a double helix by the bonds between base pairs.

^ Dynamics of the B-A transition of DNA double helices.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

This triple-stranded structure is called a displacement loop or D-loop.[45]
Branch-dna.png Multi-branch-dna.png
Single branch Multiple branches
Branched DNA can form networks containing multiple branches.

Branched DNA

.In DNA fraying occurs when non-complementary regions exist at the end of an otherwise complementary double-strand of DNA. However, branched DNA can occur if a third strand of DNA is introduced and contains adjoining regions able to hybridize with the frayed regions of the pre-existing double-strand.^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The method of claim 2, wherein said double stranded DNA consists of the sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Accordingly, the invention includes kits containing (i.e.,comprising) one or more dsDNA epitopes, preferably polynucleotides (preferably, double stranded (ds) DNA molecules) comprising an epitope which binds to an anti-ds DNA antibody from an individual (and the epitope-containing polynucleotide binds to ananti-ds DNA antibody from an individual).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

.Although the simplest example of branched DNA involves only three strands of DNA, complexes involving additional strands and multiple branches are also possible.^ In a preferred embodiment, the dsDNA epitope (such as a polynucleotide, for example, double stranded DNA) is biotinylated.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[48] Branched DNA can be used in nanotechnology to construct geometric shapes, see the section on uses in technology below.

Chemical modifications

Cytosine chemical structure.png 5-methylcytosine.png Thymine chemical structure.png
cytosine 5-methylcytosine thymine
Structure of cytosine with and without the 5-methyl group. Deamination converts 5-methylcytosine into thymine.

Base modifications

.The expression of genes is influenced by how the DNA is packaged in chromosomes, in a structure called chromatin.^ DNA packaging: The folding of an organism's DNA molecule into a compact, orderly structure that fits within the limited space of a CELL or VIRUS PARTICLE. MeSH 2004 .

^ A technique called electrophoresis is used to obtain DNA profiles, relying on sections of our DNA The structure of DNA is illustrated .
  • Definition: DNA from Online Medical Dictionary 20 September 2009 11:58 UTC dvfreelancer.com [Source type: FILTERED WITH BAYES]

^ The expression of genes is influenced by the chromatin structure of a chromosome, and regions of heterochromatin (with little or no gene expression) correlate with the methylation of cytosine .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.Base modifications can be involved in packaging, with regions that have low or no gene expression usually containing high levels of methylation of cytosine bases.^ In contrast, FIG. 17 shows the entire patient population pool (i.e., the "intent to treat" population) which contains both low and high affinity patients.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

For example, cytosine methylation, produces 5-methylcytosine, which is important for X-chromosome inactivation.[49] The average level of methylation varies between organisms - the worm Caenorhabditis elegans lacks cytosine methylation, while vertebrates have higher levels, with up to 1% of their DNA containing 5-methylcytosine.[50] Despite the importance of 5-methylcytosine, it can deaminate to leave a thymine base, methylated cytosines are therefore particularly prone to mutations.[51] .Other base modifications include adenine methylation in bacteria, the presence of 5-hydroxymethylcytosine in the brain,[52] and the glycosylation of uracil to produce the "J-base" in kinetoplastids.^ Preferably, the polynucleotide is DNA. As used herein, "DNA" includes not only bases A, T, C, and G, but also includes any of their analogs or modified forms of these bases, such as methylated nucleotides, internucleotide modifications such asuncharged linkages and thioates, use of sugar analogs, and modified and/or alternative backbone structures, such as polyamides.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[53][54]

Damage

A covalent adduct between benzo[a]pyrene, the major mutagen in tobacco smoke, and DNA[55]
DNA can be damaged by many sorts of mutagens, which change the DNA sequence. Mutagens include oxidizing agents, alkylating agents and also high-energy electromagnetic radiation such as ultraviolet light and X-rays. .The type of DNA damage produced depends on the type of mutagen.^ "Bipyrimidine photoproducts rather than oxidative lesions are the main type of DNA damage involved in the genotoxic effect of solar ultraviolet radiation".
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ SOS induction could not elicit iSDR Homologous recombination-dependent initiation of DNA replication from DNA damage-inducible origins in Escherichia coli.
  • WikiGenes - recA - DNA strand exchange and recombination... 19 November 2009 18:56 UTC www.wikigenes.org [Source type: Academic]

^ Mutagens are agents which can produce genetic mutations - these are alterations of one DNA base to another base.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

For example, UV light can damage DNA by producing thymine dimers, which are cross-links between pyrimidine bases.[56] .On the other hand, oxidants such as free radicals or hydrogen peroxide produce multiple forms of damage, including base modifications, particularly of guanosine, and double-strand breaks.^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Preferably, the polynucleotide is DNA. As used herein, "DNA" includes not only bases A, T, C, and G, but also includes any of their analogs or modified forms of these bases, such as methylated nucleotides, internucleotide modifications such asuncharged linkages and thioates, use of sugar analogs, and modified and/or alternative backbone structures, such as polyamides.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ This is done, for example, by conjugating the polynucleotide to the valency platform molecule at apredetermined site on the polynucleotide chain such that the polynucleotide forms a pendant chain of at least about 20 base pairs measured from the conjugating site to the free (unattached) end of the chain.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[57] .A typical human cell contains about 150,000 bases that have suffered oxidative damage.^ Preferred polymers are based on polyethylene glycols (PEGs) having a molecularweight of about 200 to about 8,000.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[58] .Of these oxidative lesions, the most dangerous are double-strand breaks, as these are difficult to repair and can produce point mutations, insertions and deletions from the DNA sequence, as well as chromosomal translocations.^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The method of claim 2, wherein said double stranded DNA consists of the sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Preferably, the dsDNA epitopesare polynucleotides, said polynucleotide preferably comprising, consisting essentially of or consisting of the double stranded DNA sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[59]
Many mutagens fit into the space between two adjacent base pairs, this is called intercalating. Most intercalators are aromatic and planar molecules, and include Ethidium bromide, daunomycin, and doxorubicin. .In order for an intercalator to fit between base pairs, the bases must separate, distorting the DNA strands by unwinding of the double helix.^ Each DNA is a double stranded helix where the strands are linked by hydrogen bonds (Base Pairs) between guamine & cytosine, thymine & adenine.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ DNA - double helix .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

^ DNA double helix 7-038 .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

.This inhibits both transcription and DNA replication, causing toxicity and mutations.^ These structural modifications inhibit transcription and replication processes, causing both toxicity and mutations.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ A number of environmental agents such as radiation (UV, X-rays, radioactive elements) and chemicals (pesticides, cigarette smoke) can cause mutations (changes) in DNA. .

^ The configuration of the DNA molecule is highly stable, allowing it to act as a template for the replication of new DNA molecules, as well as for the production (transcription) of the related RNA ( ribonucleic acid ) molecule.
  • DNA (chemical compound) -- Britannica Online Encyclopedia 19 January 2010 18:22 UTC www.britannica.com [Source type: Academic]

As a result, DNA intercalators are often carcinogens, and Benzo[a]pyrene diol epoxide, acridines, aflatoxin and ethidium bromide are well-known examples.[60][61][62] .Nevertheless, due to their ability to inhibit DNA transcription and replication, other similar toxins are also used in chemotherapy to inhibit rapidly growing cancer cells.^ In other embodiments, the kits comprise the conjugates described herein, with instructions for using the conjugate to detect affinity of anindividual's anti-ds DNA antibodies for the conjugate.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The polynucleotides may be isolated from the other DNA of the cell/microorganism by treatment with restriction enzymes andconventional size fractionation (e.g., agarose gel, Sephadex.TM. column).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Other literature describes methods which may be used in the treatment of SLE, including methods of reducing levels of circulating antibodies by inducing B cell tolerance, including, but not limited to, U.S. Pat.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[63]

Biological functions

.DNA usually occurs as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes.^ The DNA is usually in linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ In prokaryotes, chromosomal DNA is circular, and the entire genome is carried on one chromosome.

^ Another way of reducing genome size is seen in some viruses that contain linear or circular single-stranded DNA. [36] .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.The set of chromosomes in a cell makes up its genome; the human genome has approximately 3 billion base pairs of DNA arranged into 46 chromosomes.^ Human DNA has 46 chromosomes as shown in Figure 3, which is a human karyotype.
  • science tips 20 September 2009 11:58 UTC www.rpdp.net [Source type: FILTERED WITH BAYES]

^ The diploid human genome has 46 chromosomes.

^ Human DNA is about 3 billion "base" pairs long.
  • DNA Intuitive Healings 19 January 2010 8:50 UTC www.selacia.com [Source type: FILTERED WITH BAYES]

[64] The information carried by DNA is held in the sequence of pieces of DNA called genes. Transmission of genetic information in genes is achieved via complementary base pairing. .For example, in transcription, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence through the attraction between the DNA and the correct RNA nucleotides.^ DNA polymerases copy DNA sequences.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA is copied into RNA by RNA polymerases .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Some DNA sequences encode important information for the cell.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

Usually, this RNA copy is then used to make a matching protein sequence in a process called translation which depends on the same interaction between RNA nucleotides. .Alternatively, a cell may simply copy its genetic information in a process called DNA replication.^ DNA can be 'twisted' in a process called DNA supercoiling .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ When cells divide, the genetic information must be duplicated to produce two daughter copies of DNA in a process called DNA replication .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The DNA contains the genetic information of the cell.
  • DNA Intuitive Healings 19 January 2010 8:50 UTC www.selacia.com [Source type: FILTERED WITH BAYES]

.The details of these functions are covered in other articles; here we focus on the interactions between DNA and other molecules that mediate the function of the genome.^ There are many interactions that happen between DNA and other molecules to coordinate its functions.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ "Genomic DNA methylation: the mark and its mediators".
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ This topic has been covered in detail elsewhere on this website so there is no reason to repeat the information here.

Genes and genomes

.Genomic DNA is located in the cell nucleus of eukaryotes, as well as small amounts in mitochondria and chloroplasts.^ In eukaryotes, DNA is located mainly in the cell nucleus (there are also small amounts in mitochondria and chloroplasts).
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The mitochondria are organelles located outside the nucleus in the cytoplasm of the cell.

^ The DNA in the cell nucleus has a spiral structure.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid.[65] The genetic information in a genome is held within genes, and the complete set of this information in an organism is called its genotype. .A gene is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism.^ Gene--The fundamental and functional unit of heredity.
  • Norton DNA Project 19 January 2010 8:50 UTC www.nortonfamily.net [Source type: FILTERED WITH BAYES]

^ Stated another way, any character that acts as a signpost or signal of the presence or location of a gene or heredity characteristic in an individual in a population.

^ Regions of DNA sequence that have patterns that are characteristic of protein- or RNA-coding genes can be identified by gene finding algorithms, allowing researchers to predict the presence of particular gene products in an organism.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

Genes contain an open reading frame that can be transcribed, as well as regulatory sequences such as promoters and enhancers, which control the transcription of the open reading frame.
.In many species, only a small fraction of the total sequence of the genome encodes protein.^ In many species, only a small fraction of the genome encodes protein: only about 1.5% of the human genome consists of protein-coding exons, while over 50% consists of non-coding repetitive sequences .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Despite the difference in total size, the panda genome contains an estimated 21,000 genes that encode proteins, a number similar to that of humans.
  • Dna | Wired Science | Wired.com 19 January 2010 18:22 UTC www.wired.com [Source type: FILTERED WITH BAYES]

^ Otherwise, the sequence is unique to RecG and provides a signature motif that has enabled us to identify RecG-like proteins encoded in the nuclear genomes of Arabidopsis thalania and rice.
  • A model for dsDNA translocation revealed by a structural motif common to RecG and Mfd proteins : Article : The EMBO Journal 20 September 2009 12:012 UTC www.nature.com [Source type: Academic]

.For example, only about 1.5% of the human genome consists of protein-coding exons, with over 50% of human DNA consisting of non-coding repetitive sequences.^ The following are non-limiting examples of polynucleotides: a gene or gene fragment, exons, introns, mRNA, tRNA, rRNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence,isolated RNA of any sequence, nucleic acid probes, and primers.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The method of claim 2, wherein said double stranded DNA consists of the sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Preferably, the dsDNA epitopesare polynucleotides, said polynucleotide preferably comprising, consisting essentially of or consisting of the double stranded DNA sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[66] The reasons for the presence of so much non-coding DNA in eukaryotic genomes and the extraordinary differences in genome size, or C-value, among species represent a long-standing puzzle known as the "C-value enigma."[67] However, DNA sequences that do not code protein may still encode functional non-coding RNA molecules, which are involved in the regulation of gene expression.[68]
T7 RNA polymerase (blue) producing a mRNA (green) from a DNA template (orange).[69]
.Some non-coding DNA sequences play structural roles in chromosomes.^ Some non-coding DNA sequences are now known to have a structural role in chromosomes.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Quadruplex DNA: sequence, topology and structure .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ A study examined 5 polymorphic Alu Chromosomal abnormalities in which a DNA sequences are inserted into genes, disrupting the normal structure and function of those genes.
  • DNA Evidence and Molecular Genetics Disprove the Book of Mormon 19 January 2010 18:22 UTC www.godandscience.org [Source type: Academic]

.Telomeres and centromeres typically contain few genes, but are important for the function and stability of chromosomes.^ In particular, telomeres and centromeres contain few genes, but are important for the function and stability of chromosomes.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ A study examined 5 polymorphic Alu Chromosomal abnormalities in which a DNA sequences are inserted into genes, disrupting the normal structure and function of those genes.
  • DNA Evidence and Molecular Genetics Disprove the Book of Mormon 19 January 2010 18:22 UTC www.godandscience.org [Source type: Academic]

^ The definition of gene is evolving (and lengthening) as we tease apart the incredible complexity of biological and molecular processes and discover that "junk DNA" has important regulatory functions.

[43][70] .An abundant form of non-coding DNA in humans are pseudogenes, which are copies of genes that have been disabled by mutation.^ An abundant form of non-coding DNA in humans are pseudogenes , which are copies of genes that have been disabled by mutation; [10] these are usually just molecular 'fossils', but they can provide the raw genetic material for new genes.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Approximately 1.5% of human DNA codes for protein.

^ Changes in the DNA code are called mutations .

[71] These sequences are usually just molecular fossils, although they can occasionally serve as raw genetic material for the creation of new genes through the process of gene duplication and divergence.[72]

Transcription and translation

A gene is a sequence of DNA that contains genetic information and can influence the phenotype of an organism. .Within a gene, the sequence of bases along a DNA strand defines a messenger RNA sequence, which then defines one or more protein sequences.^ Within most (but not all) genes, the nucleotides define a messenger RNA (mRNA) which in turn defines one or more protein sequences.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Any base within DNA can mutate (ie.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

^ Each gene is a specific sequence of nucleotides located on one of the DNA strands.
  • science tips 16 October 2009 6:06 UTC rpdp.net [Source type: Academic]

The relationship between the nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the rules of translation, known collectively as the genetic code. .The genetic code consists of three-letter 'words' called codons formed from a sequence of three nucleotides (e.g.^ These 3 base sequences are called codons.
  • science tips 20 September 2009 11:58 UTC www.rpdp.net [Source type: FILTERED WITH BAYES]

^ The genetic code consists of three-letter 'words' called codons formed from a sequence of three nucleotides.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The only reason for these potentially very threatening diseases is that one or a few of the millions of letters in the genetic code are in the wrong place.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

ACT, CAG, TTT).
.In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase.^ DNA is copied into RNA by RNA polymerases .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ In transcription, the codons are copied into mRNA by RNA polymerase .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ It then copies the gene sequence into a mRNA transcript until it reaches a region of DNA called the terminator , where it halts and detaches from the DNA. RNA polymerase II, which transcribes most of the genes in the human genome, operates as part of a large protein complex with multiple regulatory and accessory subunits.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.This RNA copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the messenger RNA to transfer RNA, which carries amino acids.^ At the same time, another RNA copied from the DNA, called transfer RNA, carries the amino acids for the proteins to the ribosomes.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ This copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the mRNA to a specific aminoacyl-tRNA ; an amino acid carried by a transfer RNA (tRNA).
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ A defined region of DNA containing multiple copies of short sequences of bases, which are repeated a number of times, the number of repeats varying among individuals in the population.
  • Norton DNA Project 19 January 2010 8:50 UTC www.nortonfamily.net [Source type: FILTERED WITH BAYES]

Since there are 4 bases in 3-letter combinations, there are 64 possible codons (43 combinations). These encode the twenty standard amino acids, giving most amino acids more than one possible codon. .There are also three 'stop' or 'nonsense' codons signifying the end of the coding region; these are the TAA, TGA and TAG codons.^ Also, there are three stop codons that terminate polypeptide synthesis.
  • Nucleic Acids 19 January 2010 18:22 UTC www.cem.msu.edu [Source type: Academic]

^ There is one start codon (AUG) that also encodes for methionine ) and three 'stop' or 'nonsense' codons (UAA, UGA and UAG) that signify the end of the coding region.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The dashes at the beginning and end of the overall sequence shown indicate that there is more sequence available both upstream and downstream of the region shown.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

DNA replication. The double helix is unwound by a helicase and topoisomerase. Next, one DNA polymerase produces the leading strand copy. Another DNA polymerase binds to the lagging strand. This enzyme makes discontinuous segments (called Okazaki fragments) before DNA ligase joins them together.

Replication

.Cell division is essential for an organism to grow, but when a cell divides it must replicate the DNA in its genome so that the two daughter cells have the same genetic information as their parent.^ First, DNA divides into two to replicate itself.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ When cells divide, the genetic information must be duplicated to produce two daughter copies of DNA in a process called DNA replication .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The replication process on the left consists of passing information from a parent DNA molecule to daughter molecules.
  • Nucleic Acids 19 January 2010 18:22 UTC www.cem.msu.edu [Source type: Academic]

.The double-stranded structure of DNA provides a simple mechanism for DNA replication.^ The double-stranded structure of DNA provides a simple mechanism for this replication.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The precise mechanism of DNA replication is not known.

^ Linear, double-stranded DNA .

Here, the two strands are separated and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase. .This enzyme makes the complementary strand by finding the correct base through complementary base pairing, and bonding it onto the original strand.^ These pairings also referred as complementary base pairs.
  • science tips 16 October 2009 6:06 UTC rpdp.net [Source type: Academic]

^ Francis Crick and James Watson, at Cambridge University, considered hydrogen bonded base pairing interactions, and arrived at a double stranded helical model that satisfied most of the known facts, and has been confirmed by subsequent findings.
  • Nucleic Acids 19 January 2010 18:22 UTC www.cem.msu.edu [Source type: Academic]

^ These interactions together induce breakage of Watson-Crick nucleotide base pairing hydrogen bonds, resulting in bending of the DNA, strand elongation and unwinding events similar to those described for helicases (15 ).
  • Molecular Dynamics Simulations 20 November 2009 8:55 UTC www.msi.umn.edu [Source type: Academic]

.As DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction, different mechanisms are used to copy the antiparallel strands of the double helix.^ DNA double helix 7-038 .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

^ In a double helix, the direction of the nucleotides in one strand is opposite to that in the other strand.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The double-stranded structure of DNA provides a simple mechanism for this replication.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[73] In this way, the base on the old strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.

Interactions with proteins

.All the functions of DNA depend on interactions with proteins.^ Protein-DNA interaction .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

^ All of the functions of DNA depend on its interactions with proteins.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Protein-DNA interactions: a structural analysis.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

These protein interactions can be non-specific, or the protein can bind specifically to a single DNA sequence. .Enzymes can also bind to DNA and of these, the polymerases that copy the DNA base sequence in transcription and DNA replication are particularly important.^ These 3 base sequences are called codons.
  • science tips 20 September 2009 11:58 UTC www.rpdp.net [Source type: FILTERED WITH BAYES]

^ When these two DNA strands with matching sequences lock up at the right place, the helix is formed and can only be pulled apart by DNA polymerase or if the DNA itself becomes badly damaged and no longer contains large sections of bases inside its phosphate/sugar walls.
  • The DNA double helix must unwind and separate into two strands so that one strand can assemble the proper 20 September 2009 11:58 UTC askville.amazon.com [Source type: General]

^ Not all of the DNA is transcribed into RNA. Transcription starts when the RNA polymerase finds a promoter sequence on one strand of the DNA. That promoter sequence can appear on either strand; neither strand is specifically designated as the sense strand for its entire length.
  • The DNA double helix must unwind and separate into two strands so that one strand can assemble the proper 20 September 2009 11:58 UTC askville.amazon.com [Source type: General]

DNA-binding proteins

Nucleosome 2.jpg
Nucleosome (opposites attracts).JPG
.Interaction of DNA with histones (shown in white, top).^ Interaction of DNA with histones (shown in white, top).
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ These changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

These proteins' basic amino acids (below left, blue) bind to the acidic phosphate groups on DNA (below right, red).
.Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions.^ Dataset of protein-DNA complex structures .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ DNA-binding proteins .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Outline of the families of DNA-binding proteins .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.Within chromosomes, DNA is held in complexes with structural proteins.^ Dataset of protein-DNA complex structures .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Structural taxonomy and classification of protein-DNA complexes .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Protein-DNA interactions: a structural analysis.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

.These proteins organize the DNA into a compact structure called chromatin.^ Dataset of protein-DNA complex structures .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ These proteins organize the DNA into a compact structure called chromatin .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Protein-DNA interactions: a structural analysis.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

.In eukaryotes this structure involves DNA binding to a complex of small basic proteins called histones, while in prokaryotes multiple types of proteins are involved.^ Dataset of protein-DNA complex structures .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ DNA-binding proteins .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Within chromosomes, DNA is held in complexes between DNA and structural proteins.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[74][75] The histones form a disk-shaped complex called a nucleosome, which contains two complete turns of double-stranded DNA wrapped around its surface. These non-specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence.[76] .Chemical modifications of these basic amino acid residues include methylation, phosphorylation and acetylation.^ Chemical modifications of these basic amino acid residues include methylation , phosphorylation and acetylation .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Narrower terms mature peptide or protein coding sequence, signal peptide coding sequence, transit peptide coding sequence coding sequence CDS: Sequence of nucleotides that corresponds with the sequence of amino acids in a protein (location includes stop codon ).

^ Feature includes amino acid conceptual translation.

[77] .These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription.^ These changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ These observations offer an explanation as to why more than one amino acid can interact with the same nucleotide and vice-versa (11) and still satisfy site specific DNA recognition according to our hypothesis.
  • Harris et al. 20 November 2009 8:55 UTC epress.com [Source type: Academic]

^ Other transcription factors can bind enzymes that modify the histones at the promoter, this will change the accessibility of the DNA template to the polymerase.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[78] Other non-specific DNA-binding proteins in chromatin include the high-mobility group proteins, which bind to bent or distorted DNA.[79] These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that make up chromosomes.[80]
A distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication protein A is the best-understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination and DNA repair.[81] These binding proteins seem to stabilize single-stranded DNA and protect it from forming stem-loops or being degraded by nucleases.
The lambda repressor helix-turn-helix transcription factor bound to its DNA target[82]
In contrast, other proteins have evolved to bind to particular DNA sequences. The most intensively studied of these are the various transcription factors, which are proteins that regulate transcription. .Each transcription factor binds to one particular set of DNA sequences and activates or inhibits the transcription of genes that have these sequences close to their promoters.^ Codons are a sequence of DNA activated for expression.
  • DNA Intuitive Healings 19 January 2010 8:50 UTC www.selacia.com [Source type: FILTERED WITH BAYES]

^ Other proteins bind to particular DNA sequences.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Each of these proteins binds to a particular set of DNA sequences and thereby activates or inhibits the transcription of genes with these sequences close to their promoters .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.The transcription factors do this in two ways.^ Transcription factors do this in two ways.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.Firstly, they can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription.^ Some can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The sigma subunit conveys promoter specificity to RNA polymerase ; that is, it is responsible for telling RNA polymerase where to bind.
  • DNA Transcription | Learn Science at Scitable 19 January 2010 18:22 UTC www.nature.com [Source type: Academic]

^ Transcription begins when the enzyme RNA polymerase attaches to the promoter.

[83] Alternatively, transcription factors can bind enzymes that modify the histones at the promoter; this will change the accessibility of the DNA template to the polymerase.[84]
.As these DNA targets can occur throughout an organism's genome, changes in the activity of one type of transcription factor can affect thousands of genes.^ These DNA targets can occur throughout an organism's genome, so changes in the activity of one type of transcription factor in a given cell can affect the expression of many genes in that cell.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Polyploid organisms also have one genome.

^ When the DNA synthesis is complete, an error occurs in one nucleotide in a thousand.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

[85] Consequently, these proteins are often the targets of the signal transduction processes that control responses to environmental changes or cellular differentiation and development. .The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to "read" the DNA sequence.^ The edges of the bases are more accessible in the major groove, so proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Protein-DNA interaction .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

^ Scientists reading DNA sequence .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

.Most of these base-interactions are made in the major groove, where the bases are most accessible.^ Most of these interactions occur in the major groove, where the bases are most accessible.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The control simulation does not display a decrease in overall solvent-accessible area, the minor groove does not increase in area, and the major groove compresses minimally.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

^ These backbone interactions are reported to contribute to the protein's DNA binding affinity and to position the DNA recognition helices within their cognate operator DNA major groove halfsites (1 ).
  • Molecular Dynamics Simulations 20 November 2009 8:55 UTC www.msi.umn.edu [Source type: Academic]

[86]
The restriction enzyme EcoRV (green) in a complex with its substrate DNA[87]

DNA-modifying enzymes

Nucleases and ligases

Nucleases are enzymes that cut DNA strands by catalyzing the hydrolysis of the phosphodiester bonds. Nucleases that hydrolyse nucleotides from the ends of DNA strands are called exonucleases, while endonucleases cut within strands. The most frequently used nucleases in molecular biology are the restriction endonucleases, which cut DNA at specific sequences. .For instance, the EcoRV enzyme shown to the left recognizes the 6-base sequence 5′-GAT|ATC-3′ and makes a cut at the vertical line.^ For instance, the EcoRV enzyme recognizes the 6-base sequence 5′-GAT|ATC-3′ and makes a cut at the vertical line.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Endonuclease Fok I is a bipartite restriction enzyme which recognizes a specific DNA sequence and non-specifically cleaves at a position a short distance away.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ As noted in the 2'-deoxycytidine structure on the left, the numbering of the sugar carbons makes use of primed numbers to distinguish them from the heterocyclic base sites.
  • Nucleic Acids 19 January 2010 18:22 UTC www.cem.msu.edu [Source type: Academic]

In nature, these enzymes protect bacteria against phage infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the restriction modification system.[88] In technology, these sequence-specific nucleases are used in molecular cloning and DNA fingerprinting.
Enzymes called DNA ligases can rejoin cut or broken DNA strands.[89] Ligases are particularly important in lagging strand DNA replication, as they join together the short segments of DNA produced at the replication fork into a complete copy of the DNA template. They are also used in DNA repair and genetic recombination.[89]

Topoisomerases and helicases

Topoisomerases are enzymes with both nuclease and ligase activity. These proteins change the amount of supercoiling in DNA. Some of these enzymes work by cutting the DNA helix and allowing one section to rotate, thereby reducing its level of supercoiling; the enzyme then seals the DNA break.[27] .Other types of these enzymes are capable of cutting one DNA helix and then passing a second strand of DNA through this break, before rejoining the helix.^ In a double helix, the direction of the nucleotides in one strand is opposite to that in the other strand.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Others can cut one DNA helix and then pass a second strand of DNA through this break, before rejoining the helix.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Topoisomerase : This enzyme initiates unwinding of the double helix by cutting one of the strands.
  • Nucleic Acids 19 January 2010 18:22 UTC www.cem.msu.edu [Source type: Academic]

[90] .Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.^ Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA replication is bidirectional (There are two replication forks per circular DNA genome and replication involves leading/lagging strands, Okazaki fragments , DNA ligase , etc.

^ Topoisomerases I promote the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of DNA replication, transcription and recombination.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[28]
Helicases are proteins that are a type of molecular motor. They use the chemical energy in nucleoside triphosphates, predominantly ATP, to break hydrogen bonds between bases and unwind the DNA double helix into single strands.[91] .These enzymes are essential for most processes where enzymes need to access the DNA bases.^ Given that these proteins also promote DNA repair very effectively, we conclude that neither F620 nor E634 is essential for RecG helicase activity.
  • A model for dsDNA translocation revealed by a structural motif common to RecG and Mfd proteins : Article : The EMBO Journal 20 September 2009 12:012 UTC www.nature.com [Source type: Academic]

^ In prokaryotes the reaction is most commonly found in the protection of the DNA from restriction enzymes.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Although all these processes take place at such a dazzling speed-3,000 base pairs are produced in a minute,-all these pairs are checked repeatedly by the enzymes in charge and the necessary amendments are made.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

Polymerases

Polymerases are enzymes that synthesize polynucleotide chains from nucleoside triphosphates. .The sequence of their products are copies of existing polynucleotide chains - which are called templates.^ When a cell uses the information in a gene, the DNA sequence is copied into a complementary single strand of RNA in a process called transcription .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA polymerases synthesize DNA strands by catalyzing the stepwise addition of a deoxyribonuleotide to the 3'-OH end of a polynucleotide chain that is paired to a second, template stand.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ A DNA sequence is called a "sense" sequence if it is copied by these enzymes (which only work in the 5' to 3' direction) and then translated into protein.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.These enzymes function by adding nucleotides onto the 3′ hydroxyl group of the previous nucleotide in a DNA strand.^ They add nucleotides onto the 3′ hydroxyl group of the previous nucleotide in the DNA strand, so all polymerases work in a 5′ to 3′ direction.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ In transcription (#1 on Figure 2), mRNA transcribes, or copies down a gene from DNA. An enzyme called RNA polymerase opens the necessary gene in the DNA and begins adding complimentary nucleotides to “copy” the gene base sequence.
  • science tips 20 September 2009 11:58 UTC www.rpdp.net [Source type: FILTERED WITH BAYES]

^ But what if the enzymes do not know how to repair a particular strand of DNA. It is not working properly and the enzymes cannot make the repair.

.Consequently, all polymerases work in a 5′ to 3′ direction.^ They add nucleotides onto the 3′ hydroxyl group of the previous nucleotide in the DNA strand, so all polymerases work in a 5′ to 3′ direction.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[92] .In the active site of these enzymes, the incoming nucleoside triphosphate base-pairs to the template: this allows polymerases to accurately synthesize the complementary strand of their template.^ Polymerases synthesise polynucleotides from nucleoside triphosphates .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA polymerase binds to one strand of the DNA, reads the sequence of bases on the template strand and then synthesises the complementary strand.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ In the active site of these enzymes, the nucleoside triphosphate substrate base-pairs to a single-stranded polynucleotide template: this allows polymerases to synthesise the complementary strand of this template accurately.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.Polymerases are classified according to the type of template that they use.^ The α-proteins translated in the cytoplasm are transported into nucleus where they enable the beta-promoters to be used by the host RNA polymerase (figure 16).

^ They use various types of pipetting equipment and various methods of moving the cells on the agar surface.
  • Laboratory Methods 16 January 2010 1:27 UTC www.phys.ksu.edu [Source type: FILTERED WITH BAYES]

In DNA replication, a DNA-dependent DNA polymerase makes a copy of a DNA sequence. Accuracy is vital in this process, so many of these polymerases have a proofreading activity. .Here, the polymerase recognizes the occasional mistakes in the synthesis reaction by the lack of base pairing between the mismatched nucleotides.^ DNA(Instructions)> RNA(Messenger)> Protein(Synthesis - 3000 gene base pairs may contain 1000 amino acids).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ Many mutagens intercalate into the space between two adjacent base pairs.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

If a mismatch is detected, a 3′ to 5′ exonuclease activity is activated and the incorrect base removed.[93] In most organisms DNA polymerases function in a large complex called the replisome that contains multiple accessory subunits, such as the DNA clamp or helicases.[94]
RNA-dependent DNA polymerases are a specialized class of polymerases that copy the sequence of an RNA strand into DNA. They include reverse transcriptase, which is a viral enzyme involved in the infection of cells by retroviruses, and telomerase, which is required for the replication of telomeres.[42][95] .Telomerase is an unusual polymerase because it contains its own RNA template as part of its structure.^ Telomerase is an unusual polymerase because it contains its own RNA template as part of its structure.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The nucleolus organizer is a cytological structure that contains the ribosomal RNA genes.
  • MGI-Guidelines for Nomenclature of Genes, Genetic Markers, Alleles, & Mutations in Mouse & Rat 16 January 2010 1:27 UTC www.informatics.jax.org [Source type: Academic]

^ [NCBI] Single-stranded complementary DNA synthesized from an RNA template by the action of RNA- dependent DNA polymerase.

[43]
.Transcription is carried out by a DNA-dependent RNA polymerase that copies the sequence of a DNA strand into RNA. To begin transcribing a gene, the RNA polymerase binds to a sequence of DNA called a promoter and separates the DNA strands.^ DNA polymerases copy DNA sequences.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The two strands of DNA separate, and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ [The promoter is a short sequence of DNA that defines the start of a gene, the direction of transcription, and the strand of DNA to be transcribed.

It then copies the gene sequence into a messenger RNA transcript until it reaches a region of DNA called the terminator, where it halts and detaches from the DNA. As with human DNA-dependent DNA polymerases, RNA polymerase II, the enzyme that transcribes most of the genes in the human genome, operates as part of a large protein complex with multiple regulatory and accessory subunits.[96]

Genetic recombination

Holliday Junction cropped.png
Holliday junction coloured.png
Structure of the Holliday junction intermediate in genetic recombination. .The four separate DNA strands are coloured red, blue, green and yellow.^ DNA red blue .
  • Double helix Illustrations and Clipart. 107 Double helix royalty free illustrations, and drawings available to search from over 15 stock vector EPS clip art graphics publishers. 20 September 2009 11:58 UTC www.fotosearch.com [Source type: General]

^ These interactions together induce DNA bending, strand separation and unwinding events which are associated with DNA transcription.
  • Molecular Dynamics Simulations 20 November 2009 8:55 UTC www.msi.umn.edu [Source type: Academic]

^ The DNA-binding region of the Tus family is made of four antiparallel ß strands (colored red in Figure 6b ) which links the amino- and carboxy-terminal domains and produces a large central cleft in the protein.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[97]
Recombination involves the breakage and rejoining of two chromosomes (M and F) to produce two re-arranged chromosomes (C1 and C2).
A DNA helix usually does not interact with other segments of DNA, and in human cells the different chromosomes even occupy separate areas in the nucleus called "chromosome territories".[98] This physical separation of different chromosomes is important for the ability of DNA to function as a stable repository for information, as one of the few times chromosomes interact is during chromosomal crossover when they recombine. .Chromosomal crossover is when two DNA helices break, swap a section and then rejoin.^ Recombination is when two DNA helices break, swap a section and then rejoin.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The two -helices comprising the helical hairpin are distant from the proposed binding site for the dsDNA on which RecG translocates, and are therefore very unlikely to contact DNA directly.
  • A model for dsDNA translocation revealed by a structural motif common to RecG and Mfd proteins : Article : The EMBO Journal 20 September 2009 12:012 UTC www.nature.com [Source type: Academic]

^ When a cell is getting ready to divide creating two daughter cells, it packs its DNA into bundles called chromosomes.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

.Recombination allows chromosomes to exchange genetic information and produces new combinations of genes, which increases the efficiency of natural selection and can be important in the rapid evolution of new proteins.^ The genetic material in our chromosomes is a combination of genes from our parents.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ The existence of a gene can also be inferred in the absence of any genetic or physical map information, such as from a cDNA sequence.
  • MGI-Guidelines for Nomenclature of Genes, Genetic Markers, Alleles, & Mutations in Mouse & Rat 16 January 2010 1:27 UTC www.informatics.jax.org [Source type: Academic]

^ While the gene name should ideally be informative as to the function or nature of the gene, care should be taken to avoid putting inaccurate information in the name.
  • MGI-Guidelines for Nomenclature of Genes, Genetic Markers, Alleles, & Mutations in Mouse & Rat 16 January 2010 1:27 UTC www.informatics.jax.org [Source type: Academic]

[99] .Genetic recombination can also be involved in DNA repair, particularly in the cell's response to double-strand breaks.^ Genetic recombination can also be involved in DNA repair.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ "The role of double-strand break repair - insights from human genetics".
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The DNA contains the genetic information of the cell.
  • DNA Intuitive Healings 19 January 2010 8:50 UTC www.selacia.com [Source type: FILTERED WITH BAYES]

[100]
The most common form of chromosomal crossover is homologous recombination, where the two chromosomes involved share very similar sequences. .Non-homologous recombination can be damaging to cells, as it can produce chromosomal translocations and genetic abnormalities.^ However, recombination can also damage cells, by producing chromosomal translocations and genetic abnormalities.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Mutations that are the result of gene targeting by homologous recombination in ES cells are given the symbol of the targeted gene, with a superscript consisting of three parts: the symbol tm to denote a targeted mutation, a serial number from the laboratory of origin and the Laboratory code where the mutation was produced (see Section 2.1 ).
  • MGI-Guidelines for Nomenclature of Genes, Genetic Markers, Alleles, & Mutations in Mouse & Rat 16 January 2010 1:27 UTC www.informatics.jax.org [Source type: Academic]

^ When cells divide, the genetic information must be duplicated to produce two daughter copies of DNA in a process called DNA replication .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

The recombination reaction is catalyzed by enzymes known as recombinases, such as RAD51.[101] The first step in recombination is a double-stranded break either caused by an endonuclease or damage to the DNA.[102] A series of steps catalyzed in part by the recombinase then leads to joining of the two helices by at least one Holliday junction, in which a segment of a single strand in each helix is annealed to the complementary strand in the other helix. .The Holliday junction is a tetrahedral junction structure that can be moved along the pair of chromosomes, swapping one strand for another.^ The Holliday junction is a tetrahedral junction structure which can be moved along the pair of chromosomes, swapping one strand for another.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ T ransposons are genes that move from one location to another on a chromosome.

^ Complementary primary nucleotide structures for each strand allowed intra-strand hydrogen bonding between each pair of bases.
  • Nucleic Acids 19 January 2010 18:22 UTC www.cem.msu.edu [Source type: Academic]

The recombination reaction is then halted by cleavage of the junction and re-ligation of the released DNA.[103]

Evolution

.DNA contains the genetic information that allows all modern living things to function, grow and reproduce.^ DNA contains the genetic information that is the basis for living functions including growth, reproduction and evolution.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The DNA contains the genetic information of the cell.
  • DNA Intuitive Healings 19 January 2010 8:50 UTC www.selacia.com [Source type: FILTERED WITH BAYES]

^ DNA Structure Just a little less than a century ago, scientists were still trying to figure out what molecule held genetic information.
  • science tips 20 September 2009 11:58 UTC www.rpdp.net [Source type: FILTERED WITH BAYES]

.However, it is unclear how long in the 4-billion-year history of life DNA has performed this function, as it has been proposed that the earliest forms of life may have used RNA as their genetic material.^ DNA(Instructions)> RNA(Messenger)> Protein(Synthesis - 3000 gene base pairs may contain 1000 amino acids).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ An alternative to the ribose strategy is forming aldehyde functionalities on the polynucleotides and using those functionalities to couple the polynucleotide to the platform molecule via reactive functional groups thereon.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ A complete structural representation of a segment of the RNA polymer formed from 5'-nucleotides may be viewed by clicking on the above diagram .
  • Nucleic Acids 19 January 2010 18:22 UTC www.cem.msu.edu [Source type: Academic]

[92][104] RNA may have acted as the central part of early cell metabolism as it can both transmit genetic information and carry out catalysis as part of ribozymes.[105] This ancient RNA world where nucleic acid would have been used for both catalysis and genetics may have influenced the evolution of the current genetic code based on four nucleotide bases. This would occur since the number of different bases in such an organism is a trade-off between a small number of bases increasing replication accuracy and a large number of bases increasing the catalytic efficiency of ribozymes.[106]
.Unfortunately, there is no direct evidence of ancient genetic systems, as recovery of DNA from most fossils is impossible.^ A Cameron Connection : DNA match, with no genetic distance, to Participant #48924 .
  • Cameron DNA Project - Results 19 January 2010 18:22 UTC www.clan-cameron.org [Source type: FILTERED WITH BAYES]

^ In bacteria , there is no nuclear membrane around the DNA, which is in a region called the nucleoid .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Participant #33561 Paternal Line: A Cameron Connection : DNA match, with no genetic distance, to Participant #29328 .
  • Cameron DNA Project - Results 19 January 2010 18:22 UTC www.clan-cameron.org [Source type: FILTERED WITH BAYES]

.This is because DNA will survive in the environment for less than one million years and slowly degrades into short fragments in solution.^ Larger DNA fragments are degraded before smaller ones.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

^ Over 400 fragments of the skull Australopithecus- Zinjanthropus Boisei were found in 1911, but it was only in 1959 when Mary Leakey uncovered a 1.75 million year old australopithecus jawbone.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ When viewed in a standard 13 x 100 mm tube, yeast suspensions of less than about 1 million cells per ml are not visibly turbid.
  • Laboratory Methods 16 January 2010 1:27 UTC www.phys.ksu.edu [Source type: FILTERED WITH BAYES]

[107] Claims for older DNA have been made, most notably a report of the isolation of a viable bacterium from a salt crystal 250 million years old,[108] but these claims are controversial.[109][110]

Uses in technology

Genetic engineering

Methods have been developed to purify DNA from organisms, such as phenol-chloroform extraction and manipulate it in the laboratory, such as restriction digests and the polymerase chain reaction. .Modern biology and biochemistry make intensive use of these techniques in recombinant DNA technology.^ These changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Perhaps you are simply tuning into something in the mass consciousness about the earlier tampering with DNA, and this makes you wary of any modern day DNA work.
  • DNA Intuitive Healings 19 January 2010 8:50 UTC www.selacia.com [Source type: FILTERED WITH BAYES]

^ Using genetic similarity search and secondary structure prediction techniques, we were successful in being the first to locate and describe the GR DNA recognition helix (5 , 11).
  • Molecular Dynamics Simulations 20 November 2009 8:55 UTC www.msi.umn.edu [Source type: Academic]

Recombinant DNA is a man-made DNA sequence that has been assembled from other DNA sequences. They can be transformed into organisms in the form of plasmids or in the appropriate format, by using a viral vector.[111] The genetically modified organisms produced can be used to produce products such as recombinant proteins, used in medical research,[112] or be grown in agriculture.[113][114]

Forensics

Forensic scientists can use DNA in blood, semen, skin, saliva or hair found at a crime scene to identify a matching DNA of an individual, such as a perpetrator. This process is called genetic fingerprinting, or more accurately, DNA profiling. In DNA profiling, the lengths of variable sections of repetitive DNA, such as short tandem repeats and minisatellites, are compared between people. This method is usually an extremely reliable technique for identifying a matching DNA.[115] .However, identification can be complicated if the scene is contaminated with DNA from several people.^ The ability to bend DNA is not only limited to the enzymes, however; although not as severe, DNA bending is clearly also a common feature of complexes formed by transcription factors.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[116] DNA profiling was developed in 1984 by British geneticist Sir Alec Jeffreys,[117] and first used in forensic science to convict Colin Pitchfork in the 1988 Enderby murders case.[118]
.People convicted of certain types of crimes may be required to provide a sample of DNA for a database.^ DNA samples can be collected for inclusion in a database.
  • DNA CONTROVERSY 19 January 2010 8:50 UTC www.njweedman.com [Source type: Original source]

^ People convicted of certain types of crimes may be required to provide a sample of DNA for a database.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Forensic scientists can use DNA in blood, semen, skin, saliva or hair to match samples collected at a crime scene to samples taken from possible suspects.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.This has helped investigators solve old cases where only a DNA sample was obtained from the scene.^ This has helped investigators solve old cases where only a DNA sample was obtained from the scene.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Forensic scientists can use DNA in blood, semen, skin, saliva or hair to match samples collected at a crime scene to samples taken from possible suspects.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Attorney General Peter Harvey said other states have had success in solving long-dormant homicides and other cases since implementing DNA sampling.
  • DNA CONTROVERSY 19 January 2010 8:50 UTC www.njweedman.com [Source type: Original source]

.DNA profiling can also be used to identify victims of mass casualty incidents.^ DNA profiling can also be used to identify victims of mass casualty incidents.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ These DNA variations can be used to identify people or at least distinguish one person from another.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

[119] .On the other hand, many convicted people have been released from prison on the basis of DNA techniques, which were not available when a crime had originally been committed.^ Outside the courthouse, the Weedman handed out news releases while a buddy marched around carrying a sign reading, "Say no to DNA." .
  • DNA CONTROVERSY 19 January 2010 8:50 UTC www.njweedman.com [Source type: Original source]

^ The 110,000 people already in prison or under the supervision of parole or probation officers also are to have their DNA cataloged.
  • DNA CONTROVERSY 19 January 2010 8:50 UTC www.njweedman.com [Source type: Original source]

^ We can think of an atomic property of a DNA molecule as being the statement that it contains, somewhere, the subsequence X. This is close to what many people would take to be the essence of a classical gene.
  • PLoS ONE: Beyond the Gene 16 January 2010 1:27 UTC www.plosone.org [Source type: Academic]

Bioinformatics

.Bioinformatics involves the manipulation, searching, and data mining of DNA sequence data.^ This process is also important in hybridizations involving dot strips or Southern blots where the single-stranded probes must bind accurately to their complementary target DNA sequences.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

^ The data in DNA, which is made up of 3 billion letters, is composed of a special and meaningful sequence of the letters A-T-G-C. However, not even a single letter should be misplaced in this sequence.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ For example, each cycle of PCR involves heating the DNA to separate the strands followed by cooling to the appropriate temperature to allow the primer DNAs to bind accurately to their complementary sequences.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

The development of techniques to store and search DNA sequences have led to widely applied advances in computer science, especially string searching algorithms, machine learning and database theory.[120] .String searching or matching algorithms, which find an occurrence of a sequence of letters inside a larger sequence of letters, were developed to search for specific sequences of nucleotides.^ String-searching or 'matching' algorithms, which identify a given sequence of letters inside a larger sequence of letters, are used to search for specific sequences of nucleotides.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The genetic code consists of three-letter 'words' called codons formed from a sequence of three nucleotides.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ A gene is a specific nucleotide sequence on the DNA that codes, or contains the genetic instructions, for one protein.
  • science tips 20 September 2009 11:58 UTC www.rpdp.net [Source type: FILTERED WITH BAYES]

[121] In other applications such as text editors, even simple algorithms for this problem usually suffice, but DNA sequences cause these algorithms to exhibit near-worst-case behaviour due to their small number of distinct characters. The related problem of sequence alignment aims to identify homologous sequences and locate the specific mutations that make them distinct. These techniques, especially multiple sequence alignment, are used in studying phylogenetic relationships and protein function.[122] .Data sets representing entire genomes' worth of DNA sequences, such as those produced by the Human Genome Project, are difficult to use without annotations, which label the locations of genes and regulatory elements on each chromosome.^ Maps genomic & genetic gene order: The sequential location of genes on a chromosome.

^ We now define genes as sequences of DNA that occupy specific locations on a chromosome.
  • Nucleic Acids 19 January 2010 18:22 UTC www.cem.msu.edu [Source type: Academic]

^ For example, a gene that codes eye color would be located on the same spot in two homologous chromosomes; but one of the genes may code for blue eyes on one chromosome while the other codes for brown eyes on the other chromosome.
  • science tips 20 September 2009 11:58 UTC www.rpdp.net [Source type: FILTERED WITH BAYES]

Regions of DNA sequence that have the characteristic patterns associated with protein- or RNA-coding genes can be identified by gene finding algorithms, which allow researchers to predict the presence of particular gene products in an organism even before they have been isolated experimentally.[123]

DNA nanotechnology

The DNA structure at left (schematic shown) will self-assemble into the structure visualized by atomic force microscopy at right. DNA nanotechnology is the field which seeks to design nanoscale structures using the molecular recognition properties of DNA molecules. Image from Strong, 2004.
DNA nanotechnology uses the unique molecular recognition properties of DNA and other nucleic acids to create self-assembling branched DNA complexes with useful properties.[124] .DNA is thus used as a structural material rather than as a carrier of biological information.^ DNA information is carried by four bases.

^ DNA Structure Just a little less than a century ago, scientists were still trying to figure out what molecule held genetic information.
  • science tips 20 September 2009 11:58 UTC www.rpdp.net [Source type: FILTERED WITH BAYES]

^ As a rule, information is required from multiple sources (rather than a single laboratory test) to accurately diagnose disorders associated with systemic autoantibodies.

This has led to the creation of two-dimensional periodic lattices (both tile-based as well as using the "DNA origami" method) as well as three-dimensional structures in the shapes of polyhedra.[125] Nanomechanical devices and algorithmic self-assembly have also been demonstrated,[126] and these DNA structures have been used to template the arrangement of other molecules such as gold nanoparticles and streptavidin proteins.[127]

History and anthropology

Because DNA collects mutations over time, which are then inherited, it contains historical information and by comparing DNA sequences, geneticists can infer the evolutionary history of organisms, their phylogeny.[128] This field of phylogenetics is a powerful tool in evolutionary biology. .If DNA sequences within a species are compared, population geneticists can learn the history of particular populations.^ Denes can be used to represent vastly more intricate characteristics of the DNA sequence than the simple statement that it contains a particular subsequence.
  • PLoS ONE: Beyond the Gene 16 January 2010 1:27 UTC www.plosone.org [Source type: Academic]

^ Binding of EcoP151 DNA methyltransferase to DNA reveals a large structural distortion within the recognition sequence.
  • Chemical Reagents for Investigating the Major Groove of DNA | Current Protocols 20 November 2009 8:55 UTC www.currentprotocols.com [Source type: Academic]

^ Telomeres are nucleoprotein complexes found at the ends of eukaryotic chromosomes where the DNA consists of a repeated array of short, species-specific sequence motifs.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

This can be used in studies ranging from ecological genetics to anthropology; for example, DNA evidence is being used to try to identify the Ten Lost Tribes of Israel.[129][130]
DNA has also been used to look at modern family relationships, such as establishing family relationships between the descendants of Sally Hemings and Thomas Jefferson. .This usage is closely related to the use of DNA in criminal investigations detailed above.^ Members of the same group share a prominent structural feature used for DNA recognition and are related to each other in varying degrees.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ As our main research interest lies in the investigation of interactions between proteins and DNA, the main focus is on X-ray structures of complexes that provide the requisite details.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The governor and state legislators touted the law as a way to enhance criminal investigations with a bigger database of DNA evidence.
  • DNA CONTROVERSY 19 January 2010 8:50 UTC www.njweedman.com [Source type: Original source]

.Indeed, some criminal investigations have been solved when DNA from crime scenes has matched relatives of the guilty individual.^ Forensic scientists can use DNA in blood, semen, skin, saliva or hair to match samples collected at a crime scene to samples taken from possible suspects.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ PCR-based tests are also extremely sensitive to contaminating DNA at the crime scene and within the test laboratory.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

^ The governor and state legislators touted the law as a way to enhance criminal investigations with a bigger database of DNA evidence.
  • DNA CONTROVERSY 19 January 2010 8:50 UTC www.njweedman.com [Source type: Original source]

[131]

History of DNA research

DNA was first isolated by the Swiss physician Friedrich Miescher who, in 1869, discovered a microscopic substance in the pus of discarded surgical bandages. As it resided in the nuclei of cells, he called it "nuclein".[132] In 1919, Phoebus Levene identified the base, sugar and phosphate nucleotide unit.[133] .Levene suggested that DNA consisted of a string of nucleotide units linked together through the phosphate groups.^ Since there are four kinds of nucleotides in a DNA chain, one consisting of 1,000 links could exist in 41000 forms.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ Rather than having a common structural motif for binding DNA, proteins in the enzyme group are brought together on the basis of their functions; all alter DNA structure through the catalysis of a chemical process.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The "map" consists of eight Tzolkins joined together showing relationships between the Mayan calendar, the "I Ching" and the 64 DNA codons.
  • BIRTHING THE DNA OF LIGHT 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

.However, Levene thought the chain was short and the bases repeated in a fixed order.^ An example of such a structure are short DNA intervals where the same base is tandemly repeated, as in 5'-gcAAAAAAAAAAAttg-3', or a dinucleotide or even a triplet as in 5'- ATGATGATGATGATGATGATG-3'.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

In 1937 William Astbury produced the first X-ray diffraction patterns that showed that DNA had a regular structure.[134]
In 1928, Frederick Griffith discovered that traits of the "smooth" form of the Pneumococcus could be transferred to the "rough" form of the same bacteria by mixing killed "smooth" bacteria with the live "rough" form.[135] This system provided the first clear suggestion that DNA carried genetic information—the Avery-MacLeod-McCarty experiment—when Oswald Avery, along with coworkers Colin MacLeod and Maclyn McCarty, identified DNA as the transforming principle in 1943.[136] DNA's role in heredity was confirmed in 1952, when Alfred Hershey and Martha Chase in the Hershey-Chase experiment showed that DNA is the genetic material of the T2 phage.[137]
Francis Crick
Rosalind Franklin
Raymond Gosling
In 1953 James D. Watson and Francis Crick suggested what is now accepted as the first correct double-helix model of DNA structure in the journal Nature.[7] Their double-helix, molecular model of DNA was then based on a single X-ray diffraction image (labeled as "Photo 51")[138] taken by Rosalind Franklin and Raymond Gosling in May 1952, as well as the information that the DNA bases were paired—also obtained through private communications from Erwin Chargaff in the previous years. Chargaff's rules played a very important role in establishing double-helix configurations for B-DNA as well as A-DNA.
Experimental evidence supporting the Watson and Crick model were published in a series of five articles in the same issue of Nature.[139] Of these, Franklin and Gosling's paper was the first publication of their own X-ray diffraction data and original analysis method that partially supported the Watson and Crick model[31][140]; this issue also contained an article on DNA structure by Maurice Wilkins and two of his colleagues, whose analysis and in vivo B-DNA X-ray patterns also supported the presence in vivo of the double-helical DNA configurations as proposed by Crick and Watson for their double-helix molecular model of DNA in the previous two pages of Nature.[32] In 1962, after Franklin's death, Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine.[141] Unfortunately, Nobel rules of the time allowed only living recipients, but a vigorous debate continues on who should receive credit for the discovery.[142]
In an influential presentation in 1957, Crick laid out the "Central Dogma" of molecular biology, which foretold the relationship between DNA, RNA, and proteins, and articulated the "adaptor hypothesis".[143] Final confirmation of the replication mechanism that was implied by the double-helical structure followed in 1958 through the Meselson-Stahl experiment.[144] Further work by Crick and coworkers showed that the genetic code was based on non-overlapping triplets of bases, called codons, allowing Har Gobind Khorana, Robert W. Holley and Marshall Warren Nirenberg to decipher the genetic code.[145] These findings represent the birth of molecular biology.

See also

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Further reading

  • Calladine, Chris R.; Drew, Horace R.; Luisi, Ben F. and Travers, Andrew A. (2003). Understanding DNA: the molecule & how it works. Amsterdam: Elsevier Academic Press. ISBN 0-12-155089-3. 
  • Dennis, Carina; Julie Clayton (2003). 50 years of DNA. Basingstoke: Palgrave Macmillan. ISBN 1-4039-1479-6. 
  • Judson, Horace Freeland (1996). The eighth day of creation: makers of the revolution in biology. Plainview, N.Y: CSHL Press. ISBN 0-87969-478-5. 
  • Olby, Robert C. (1994). The path to the double helix: the discovery of DNA. New York: Dover Publications. ISBN 0-486-68117-3. , first published in October 1974 by MacMillan, with foreword by Francis Crick;the definitive DNA textbook,revised in 1994 with a 9 page postscript.
  • Olby, Robert C. (2009). Francis Crick: A Biography. Plainview, N.Y: Cold Spring Harbor Laboratory Press. ISBN 0-87969-798-9. 
  • Ridley, Matt (2006). Francis Crick: discoverer of the genetic code. [Ashland, OH: Eminent Lives, Atlas Books. ISBN 0-06-082333-X. 
  • Berry, Andrew; Watson, James D. (2003). DNA: the secret of life. New York: Alfred A. Knopf. ISBN 0-375-41546-7. 
  • Stent, Gunther Siegmund; Watson, James D. (1980). The double helix: a personal account of the discovery of the structure of DNA. New York: Norton. ISBN 0-393-95075-1. 
  • Wilkins, Maurice (2003). The third man of the double helix the autobiography of Maurice Wilkins. Cambridge, Eng: University Press. ISBN 0-19-860665-6. 

External links

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Wiktionary

Up to date as of January 15, 2010

Definition from Wiktionary, a free dictionary

See also dna

Contents

English

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Initialism

DNA
  1. A substance inherent in living beings which determines their form, and can be used to uniquely identify a person.
  2. (genetics) deoxyribonucleic acid, the genetic material of nearly all forms of life.
  3. (biochemistry) A biopolymer of deoxyribonucleic acids (a type of nucleic acid) that has four different chemical groups, called bases: adenine, guanine, cytosine, and thymine.
  4. Defense Nuclear Agency.
  5. Did Not Answer.
  6. Did Not Arrive (used when someone fails to keep an appointment).
  7. Did Not Attend.
  8. Do Not Assume.
  9. Drugs 'n' alcohol.

Derived terms

Related terms

Translations

Anagrams


French

Abbreviation

DNA
  1. Dernière Nouvelles d'Alsace ("Latest News from Alsace"), a French periodical.

Anagrams

  • Anagrams of ADN

Turkish

Abbreviation

DNA
  1. "Deoksiribonükleik asit", deoxyribonucleic acid, the genetic material of nearly all forms of life.

Genealogy

Up to date as of February 01, 2010

From Familypedia

The structure of part of a DNA double helix
.Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms.^ Deoxyribonucleic acid: the chemical inside the nucleus of a cell that carries the genetic instructions for making living organisms.
  • DNA Evidence and Molecular Genetics Disprove the Book of Mormon 19 January 2010 18:22 UTC www.godandscience.org [Source type: Academic]

^ An all-atom empirical energy function for the simulation of nucleic acids.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

^ This Deoxyribonucleic acid: the chemical inside the nucleus of a cell that carries the genetic instructions for making living organisms.
  • DNA Evidence and Molecular Genetics Disprove the Book of Mormon 19 January 2010 18:22 UTC www.godandscience.org [Source type: Academic]

.The main role of DNA molecules is the long-term storage of information and DNA is often compared to a set of blueprints, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules.^ When the need is felt for a protein in a cell, a signal is sent to the DNA molecule.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ This scenario proposed that, not proteins, but rather the RNA molecules that contained the information for proteins were formed first.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ How is a 1 metre long DNA molecule contained in such a tiny space?
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

.The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.^ Genetic recombination can also be involved in DNA repair.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA information is carried by four bases.

^ Quadruplex DNA: sequence, topology and structure .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.Chemically, DNA is a long polymer of simple units called nucleotides, with a backbone made of sugars and phosphate groups joined by ester bonds.^ DNA is a long polymer of simple units called nucleotides , held together by a sugar phosphate backbone.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ DNA is a long chain of repeating units called nucleotides (a nucleotide is a base linked to a sugar and one or more phosphate groups) [15] The DNA chain is 22-26 Å wide (2.2-2.6nm) [16] The nucleotides are very small (just 3.3Å long), but DNA can contain millions of them: the DNA in the largest human chromosome (Chromosome 1) has 220 million base pairs.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.Attached to each sugar is one of four types of molecules called bases.^ LJP 394 is composed of four 20-mer dsDNA epitopes that are covalently attached to a triethyleneglycol-based platform by a thiol linkage.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The complexes were defined as any structure containing one or more protein chains and at least one double-stranded DNA of more than four base-pairs (bp) in length.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ An epitope which is "conjugated" to a valency platform molecule is one that is attached to the valency platform molecule, either by covalent and/or non-covalent interactions.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

.It is the sequence of these four bases along the backbone that encodes information.^ The sequence of these four bases encodes the information and is the genetic code of all of us ( more information ...
  • Home - DNA rainbow 19 January 2010 18:22 UTC www.dna-rainbow.org [Source type: FILTERED WITH BAYES]

^ DNA information is carried by four bases.

^ Scientists use these base sequences to locate the position of genes on chromosomes and to construct a map of the entire human genome.
  • DNA Molecule - Picture - ninemsn Encarta 16 October 2009 6:06 UTC au.encarta.msn.com [Source type: Academic]

.This information is read using the genetic code, which specifies the sequence of the amino acids within proteins.^ This is possible because of the genetic code which translates the nucleic acid sequence to an amino-acid sequence.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ These four specify a particular amino acid used in making a protein.

^ DNA(Instructions)> RNA(Messenger)> Protein(Synthesis - 3000 gene base pairs may contain 1000 amino acids).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

.The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.^ DNA is copied into RNA by RNA polymerases .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ When a cell uses the information in a gene, the DNA sequence is copied into a complementary single strand of RNA in a process called transcription .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA can be 'twisted' in a process called DNA supercoiling .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.Most of these RNA molecules are used to synthesize proteins, but others are used directly in structures such as ribosomes and spliceosomes.^ Preferably, the polynucleotide is DNA. As used herein, "DNA" includes not only bases A, T, C, and G, but also includes any of their analogs or modified forms of these bases, such as methylated nucleotides, internucleotide modifications such asuncharged linkages and thioates, use of sugar analogs, and modified and/or alternative backbone structures, such as polyamides.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ As described herein, peptide(s) that are immunoreactive with dsDNA and are derived from the human ribosomal protein S1 can be used to induce tolerance in a patient.

^ Let us forget all the impossibilities for a moment and suppose that a protein molecule was formed in the most inappropriate, most uncontrolled environment such as the primordial earth conditions.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

.Within cells, DNA is organized into structures called chromosomes.^ The DNA in the cell nucleus has a spiral structure.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ Within chromosomes, DNA is held in complexes between DNA and structural proteins.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ These proteins organize the DNA into a compact structure called chromatin .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.These chromosomes are duplicated before cells divide, in a process called DNA replication.^ DNA can be 'twisted' in a process called DNA supercoiling .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ When cells divide, the genetic information must be duplicated to produce two daughter copies of DNA in a process called DNA replication .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ What happens to DNA at the end of this dividing process?
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

.Eukaryotic organisms such as animals, plants, and fungi store their DNA inside the cell nucleus, while in prokaryotes such as bacteria it is found in the cell's cytoplasm.^ In animals and plants, most DNA is stored inside the cell nucleus .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The DNA in the cell nucleus has a spiral structure.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ In eukaryotes (organisms such as plants, yeasts and animals whose cells have a nucleus) DNA usually occurs as several large, linear chromosomes , each of which may contain hundreds or thousands of genes.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.Within the chromosomes, chromatin proteins such as histones compact and organize DNA, which helps control its interactions with other proteins and thereby control which genes are transcribed.^ DNA in chromatin is organized in arrays of nucleosomes.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ DNA(Instructions)> RNA(Messenger)> Protein(Synthesis - 3000 gene base pairs may contain 1000 amino acids).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ During DNA Recoding, you will find fairly high levels of excreted proteins in body fluids such as urine.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

Contents

Physical and chemical properties

The chemical structure of DNA.
.DNA is a long polymer made from repeating units called nucleotides.^ DNA is a long polymer of simple units called nucleotides , held together by a sugar phosphate backbone.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Nucleases cut DNA strands by catalyzing the hydrolysis of the phosphodiester bonds (nucleases that hydrolyse nucleotides from the ends of DNA strands are called exonucleases , while endonucleases cut within strands).
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ If many nucleotides are linked together, as in DNA, the polymer is referred to as a polynucleotide .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[1][2] .The DNA chain is 22 to 26 Ångströms wide (2.2 to 2.6 nanometres), and one nucleotide unit is 3.3 Ångstroms (0.33 nanometres) long.^ DNA is the long two stranded chain.

^ Line 4 : Each DNA molecule is a long two stranded chain.

^ The final concentration of the ct DNA preparation was determined spectrophotometrically assuming an extinction coefficient of 33 .mu.g per 1 OD unit at 260 nM. .
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[3] .Although each individual repeating unit is very small, DNA polymers can be enormous molecules containing millions of nucleotides.^ DNA is composed of units called nucleotides.

^ The monomer units of DNA are nucleotides, and the polymer is known as a "polynucleotide."

^ Nucleotide: A unit from which DNA molecules are made.
  • Mutation - Changes in DNA, Causes of mutation 16 October 2009 6:06 UTC www.scienceclarified.com [Source type: Academic]

.For instance, the largest human chromosome, chromosome number 1, is 220 million base pairs long.^ DNA is a long chain of repeating units called nucleotides (a nucleotide is a base linked to a sugar and one or more phosphate groups) [15] The DNA chain is 22-26 Å wide (2.2-2.6nm) [16] The nucleotides are very small (just 3.3Å long), but DNA can contain millions of them: the DNA in the largest human chromosome (Chromosome 1) has 220 million base pairs.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Normal human chromosomes have long, G-rich telomeric overhangs at one end .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Tel (for telomere) The number of the chromosome p or q (for the short or long arm, respectively) A serial number, if more than one segment is assigned to the telomere For example, Tel4q1    telomeric sequence, Chr4, q arm 1 .
  • MGI-Guidelines for Nomenclature of Genes, Genetic Markers, Alleles, & Mutations in Mouse & Rat 16 January 2010 1:27 UTC www.informatics.jax.org [Source type: Academic]

[4]
.In living organisms, DNA does not usually exist as a single molecule, but instead as a tightly-associated pair of molecules.^ Pairs with thymine in DNA molecules.

^ Pairs with cytosine in DNA molecules.

^ In living organisms, DNA does not usually exist as a single molecule, but as a tightly-associated pair of molecules.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[5][6] .These two long strands entwine like vines, in the shape of a double helix.^ DNA is the long two stranded chain.

^ Each DNA is a double stranded helix where the strands are linked by hydrogen bonds (Base Pairs) between guamine & cytosine, thymine & adenine.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ Line 4 : Each DNA molecule is a long two stranded chain.

.The nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand in the helix.^ Line 4 : Each DNA molecule is a long two stranded chain.

^ The nucleotides joined together to form a chain.

^ In a double helix, the direction of the nucleotides in one strand is opposite to that in the other strand.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.In general, a base linked to a sugar is called a nucleoside and a base linked to a sugar and one or more phosphate groups is called a nucleotide.^ DNA is a long chain of repeating units called nucleotides (a nucleotide is a base linked to a sugar and one or more phosphate groups) [15] The DNA chain is 22-26 Å wide (2.2-2.6nm) [16] The nucleotides are very small (just 3.3Å long), but DNA can contain millions of them: the DNA in the largest human chromosome (Chromosome 1) has 220 million base pairs.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Attached to each sugar molecule is a molecule of one of four bases ; adenine (A), thymine (T), guanine (G) or cytosine (C), and the order of these bases on the DNA strand encodes information.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA is a long polymer of simple units called nucleotides , held together by a sugar phosphate backbone.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.If multiple nucleotides are linked together, as in DNA, this polymer is referred to as a polynucleotide.^ If many nucleotides are linked together, as in DNA, the polymer is referred to as a polynucleotide .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Since there are four kinds of nucleotides in a DNA chain, one consisting of 1,000 links could exist in 41000 forms.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ The nucleotide repeats contain both the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[7]
.The backbone of the DNA strand is made from alternating phosphate and sugar residues.^ One study examined, a C→T transition at One of the structural components, or building blocks, of DNA and RNA. A nucleotide consists of a base plus a molecule of sugar and one of phosphate.
  • DNA Evidence and Molecular Genetics Disprove the Book of Mormon 19 January 2010 18:22 UTC www.godandscience.org [Source type: Academic]

^ The backbone of thepolynucleotide can comprise sugars and phosphate groups (as may typically be found in RNA or DNA), or modified or substituted sugar or phosphate groups.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Each DNA has a set of nucleotides(Phosphate, Sugar(deoxyribose), Base(gaunine, cytosine), Nitrogen(Thymine, Ardenine).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

[8] .The sugar in DNA is 2-deoxyribose, which is a pentose (five carbon) sugar.^ The backbone of the DNA strand has alternating phosphate and sugar residues [21] : the sugar is the pentose (five carbon) sugar 2-deoxyribose.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ One of the major differences between DNA and RNA is the sugar: 2-deoxyribose is replaced by ribose in RNA. [19] .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Each DNA has a set of nucleotides(Phosphate, Sugar(deoxyribose), Base(gaunine, cytosine), Nitrogen(Thymine, Ardenine).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

.The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings.^ The sugar molecules are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms in the sugar rings.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The double helix is held together by hydrogen bonds between the bases attached to the two strands.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The number of H-bonds formed between all polar DNA atoms and water was calculated as a function of time for the B- to A-DNA transition in 1-ns intervals, and also for the fixed DNA simulations.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

.These asymmetric bonds mean a strand of DNA has a direction.^ Because these bonds are asymmetric, a strand of DNA has a 'direction'.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ They add nucleotides onto the 3′ hydroxyl group of the previous nucleotide in the DNA strand, so all polymerases work in a 5′ to 3′ direction.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ These proteins seem to stabilize single-stranded DNA and protect it from forming stem loops or being degraded by nucleases .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.In a double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand.^ In a double helix, the direction of the nucleotides in one strand is opposite to that in the other strand.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Thus, one DNA strand directs the synthesis of the other strand.

^ The nucleotides in one DNA strand have a specific association with the corresponding nucleotides in the other DNA strand.

.This arrangement of DNA strands is called antiparallel.^ This arrangement of DNA strands is called antiparallel .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ This strand of DNA is called the leading strand.
  • DNA Replication 19 January 2010 18:22 UTC www.contexo.info [Source type: FILTERED WITH BAYES]

^ This arrangement of the strands is called antiparallel.
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

.The asymmetric ends of DNA strands are referred to as the 5′ (five prime) and 3′ (three prime) ends.^ The asymmetric ends of a strand of DNA bases are referred to as the 5' ( five prime ) and 3' ( three prime ) ends.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The proteins consist of an incomplete five-stranded ß-barrel capped by an a helix abutting three ß strands (Figure 6e ).
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Each subunit consists of a seven-strand antiparallel ß barrel; one opening of this barrel forms a dimer interface with the equivalent segment of the other subunit while the other end points towards the DNA. .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

One of the major differences between DNA and RNA is the sugar, with 2-deoxyribose being replaced by the alternative pentose sugar ribose in RNA.[6]
.The DNA double helix is stabilized by hydrogen bonds between the bases attached to the two strands.^ Each DNA is a double stranded helix where the strands are linked by hydrogen bonds (Base Pairs) between guamine & cytosine, thymine & adenine.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ The twin is DNA. The double helix.

^ DNA is the long two stranded chain.

.The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T).^ Attached to each sugar molecule is a molecule of one of four bases ; adenine (A), thymine (T), guanine (G) or cytosine (C), and the order of these bases on the DNA strand encodes information.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Detection of single base mismatches of thymine and cytosine.
  • Chemical Reagents for Investigating the Major Groove of DNA | Current Protocols 20 November 2009 8:55 UTC www.currentprotocols.com [Source type: Academic]

^ Each DNA is a double stranded helix where the strands are linked by hydrogen bonds (Base Pairs) between guamine & cytosine, thymine & adenine.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

.These four bases are shown below and are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate.^ Preferably, the polynucleotide is DNA. As used herein, "DNA" includes not only bases A, T, C, and G, but also includes any of their analogs or modified forms of these bases, such as methylated nucleotides, internucleotide modifications such asuncharged linkages and thioates, use of sugar analogs, and modified and/or alternative backbone structures, such as polyamides.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Since there are four kinds of nucleotides in a DNA chain, one consisting of 1,000 links could exist in 41000 forms.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ The differences in the way these four different bases are set out are the reason for all the differences between people.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

.These bases are classified into two types; adenine and guanine are fused five- and six-membered heterocyclic compounds called purines, while cytosine and thymine are six-membered rings called pyrimidines.^ These bases are called codon.

^ These bases are called Adenine, Guanine, Cytosine, and Thymine.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ These genetic studies can be classified into six major groups: .
  • DNA Evidence and Molecular Genetics Disprove the Book of Mormon 19 January 2010 18:22 UTC www.godandscience.org [Source type: Academic]

[6] .A fifth pyrimidine base, called uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring.^ The amino acids brought by the tRNA take their places according to the sequence notified by the messenger RNA. Then another RNA molecule copied from DNA, called ribosomal RNA, enables the messenger and transfer RNAs to join together.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ These bases are called Adenine, Guanine, Cytosine, and Thymine.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

.Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine, but a very rare exception to this rule is a bacterial virus called PBS1 that contains uracil in its DNA.[9] In contrast, following synthesis of certain RNA molecules, a significant number of the uracils are converted to thymines by the enzymatic addition of the missing methyl group.^ A fifth pyrimidine base, uracil (U), replaces thymine in RNA. Uracil is normally only found in DNA as a breakdown product of cytosine, but bacterial viruses contain uracil in their DNA. [22] In contrast, following synthesis of certain RNA molecules, many uracils are converted to thymines.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA(Instructions)> RNA(Messenger)> Protein(Synthesis - 3000 gene base pairs may contain 1000 amino acids).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ Such coupling requires thederivatized platform molecule to have at least an equal number of amino groups as the number of polynucleotide duplexes to be bound to the platform molecule.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

.This occurs mostly on structural and enzymatic RNAs like transfer RNAs and ribosomal RNA.^ This occurs mostly on structural and enzymatic RNAs like tRNAs and ribosomal RNA .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The nucleolus organizer is a cytological structure that contains the ribosomal RNA genes.
  • MGI-Guidelines for Nomenclature of Genes, Genetic Markers, Alleles, & Mutations in Mouse & Rat 16 January 2010 1:27 UTC www.informatics.jax.org [Source type: Academic]

^ At the same time, another RNA copied from the DNA, called transfer RNA, carries the amino acids for the proteins to the ribosomes.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

[10]

Major and minor grooves

.Animation of the structure of a section of DNA. The bases lie horizontally between the two spiraling strands.^ The DNA in the cell nucleus has a spiral structure.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ DNA strands between GT or GC .
  • DNA Repair 19 January 2010 18:22 UTC users.rcn.com [Source type: Academic]

^ Hydrogen bonds between bases on opposite DNA strands .
  • Biology: Life on Earth 6E Chapter 9 -- Multiple Choice 20 September 2009 11:58 UTC cwx.prenhall.com [Source type: Academic]

Large version[11]
.The double helix is a right-handed spiral.^ DNA is illustrated by a right handed double .
  • Definition: DNA from Online Medical Dictionary 20 September 2009 11:58 UTC dvfreelancer.com [Source type: FILTERED WITH BAYES]

^ The double helix is a right-handed spiral.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The double helix in DNA consists of two right-handed polynucleotide chains that are coiled about the same axis.
  • DNA Double Helix 20 September 2009 11:58 UTC www.elmhurst.edu [Source type: Academic]

.As the DNA strands wind around each other, they leave gaps between each set of phosphate backbones, revealing the sides of the bases inside (see animation).^ DNA strands between GT or GC .
  • DNA Repair 19 January 2010 18:22 UTC users.rcn.com [Source type: Academic]

^ Modification such as DNA methylation, DNA base modification, backbone modification, and many others.
  • Custom DNA Synthesis DNA Typing DNA Chimera DNA Protein Synthesis 19 January 2010 18:22 UTC www.biosyn.com [Source type: General]

^ As the DNA strands wind around each other, gaps between the two phosphate backbones reveal the sides of the bases inside (see animation).
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.There are two of these grooves twisting around the surface of the double helix: one groove, the major groove, is 22 Å wide and the other, the minor groove, is 12 Å wide.^ It presents a major groove and a minor groove.

^ In a double helix, the direction of the nucleotides in one strand is opposite to that in the other strand.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ II.2.2 Major groove and minor groove .

[12] .The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove.^ It presents a major groove and a minor groove.

^ II.2.2 Major groove and minor groove .

^ Most of these interactions occur in the major groove, where the bases are most accessible.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.^ The first a helix is presented in the DNA major groove for binding with bases, and the second a helix makes the backbone interactions.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The edges of the bases are more accessible in the major groove, so proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Other proteins bind to particular DNA sequences.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[13]

Base pairing

.At top, a GC base pair with three hydrogen bonds.^ Each DNA is a double stranded helix where the strands are linked by hydrogen bonds (Base Pairs) between guamine & cytosine, thymine & adenine.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ Three aromatic residues from one helix intercalate into the major groove of the DNA to strikingly deform the base pair stacking (Figure 8h ).
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.At the bottom, AT base pair with two hydrogen bonds.^ Many mutagens intercalate into the space between two adjacent base pairs.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The double helix is held together by hydrogen bonds between the bases attached to the two strands.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Each DNA is a double stranded helix where the strands are linked by hydrogen bonds (Base Pairs) between guamine & cytosine, thymine & adenine.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

Hydrogen bonds are shown as dashed lines.
.Each type of base on one strand forms a bond with just one type of base on the other strand.^ Each type of base on one strand of DNA forms a bond with just one type of base on the other strand, called 'complementary base pairing '.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ "On any given day, any one of the four could have beaten the others; it was just a question of to whom the day would go that particular day."
  • Top Chef | Bravo TV Official Site 16 January 2010 1:27 UTC www.bravotv.com [Source type: FILTERED WITH BAYES]

^ The recognition sequence is often a six base pair palindromic sequence (the top DNA strand from 5' to 3' is the same as the bottom DNA strand from 5' to 3'), but others recognize four or even eight base pair sequences.
  • Restriction Enzyme Analysis of DNA-Student Handout 16 October 2009 6:06 UTC biotech.biology.arizona.edu [Source type: FILTERED WITH BAYES]

This is called complementary base pairing. .Here, purines form hydrogen bonds to pyrimidines, with A bonding only to T, and C bonding only to G. This arrangement of two nucleotides binding together across the double helix is called a base pair.^ The double helix is held together by hydrogen bonds between the bases attached to the two strands.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The two strands of DNA are held together by hydrogen bonds between bases.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Purines form hydrogen bonds to pyrimidines; for example, A bonds only to T, and C bonds only to G. This arrangement of two nucleotides joined together across the double helix is called a base pair .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.In a double helix, the two strands are also held together via forces generated by the hydrophobic effect and pi stacking, which are not influenced by the sequence of the DNA.[14] As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily.^ Hydrogen bonds can be broken and rejoined quite easily, so the two strands of DNA in a double helix can be pulled apart like a zipper, either by mechanical force or by high temperatures.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The double helix is held together by hydrogen bonds between the bases attached to the two strands.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The two strands of DNA are held together by hydrogen bonds between bases.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force or high temperature.^ Hydrogen bonds can be broken and rejoined quite easily, so the two strands of DNA in a double helix can be pulled apart like a zipper, either by mechanical force or by high temperatures.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The double-stranded structure of DNA provides a simple mechanism for this replication.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Parts of the DNA double helix that need to separate easily tend to have a high AT content, making the strands easier to pull apart.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[15] .As a result of this complementarity, all the information in the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in DNA replication.^ DNA double helix 7-038 .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

^ What is the DNA double helix?
  • genome.gov | Deoxyribonucleic Acid (DNA) 19 January 2010 18:22 UTC www.genome.gov [Source type: Academic]
  • DNA - WikiGenetics 19 January 2010 18:22 UTC www.wikigenetics.org [Source type: Academic]

^ The double-stranded structure of DNA provides a simple mechanism for this replication.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.Indeed, this reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms.^ The reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ That it had a specific base pairing.
  • DNA double helix Watson Crick Wilkins Franklin 20 September 2009 11:58 UTC www.ba-education.com [Source type: FILTERED WITH BAYES]

^ These pairings also referred as complementary base pairs.
  • science tips 16 October 2009 6:06 UTC rpdp.net [Source type: Academic]

[1]
.The two types of base pairs form different numbers of hydrogen bonds, AT forming two hydrogen bonds, and GC forming three hydrogen bonds (see figures, left).^ Note that the C-G pair has three hydrogen bonds while the A-T pair has only two, which keeps them from pairing wrong.
  • DNA Structure and Function 19 January 2010 18:22 UTC biology.clc.uc.edu [Source type: FILTERED WITH BAYES]

^ Bp : See base pair.

^ The bonds between G-C base pairs and A-T base pairs are called, hydrogen bonds.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

.The GC base pair is therefore stronger than the AT base pair.^ The complexes were defined as any structure containing one or more protein chains and at least one double-stranded DNA of more than four base-pairs (bp) in length.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The two types of base pairs form different numbers of hydrogen bonds; AT forms two hydrogen bonds, and GC forms three, so the GC base-pair is stronger than the AT pair.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determine the strength of the association between the two strands of DNA. Long DNA helices with a high GC content have stronger-interacting strands, while short helices with high AT content have weaker-interacting strands.^ Line 4 : Each DNA molecule is a long two stranded chain.

^ Dynamics of the B-A transition of DNA double helices.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

^ With each of the 6 corners there are then associated two strands of DNA., which makes 12.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

[16] .Parts of the DNA double helix that need to separate easily, such as the TATAAT Pribnow box in bacterial promoters, tend to have sequences with a high AT content, making the strands easier to pull apart.^ Parts of the DNA double helix that need to separate easily tend to have a high AT content, making the strands easier to pull apart.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The twin is DNA. The double helix.

^ Three-dimensional model of the structure of part of a DNA double helix.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[17] .In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their melting temperature (also called Tm value).^ The strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds (their ' melting temperature ').
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Purines form hydrogen bonds to pyrimidines; for example, A bonds only to T, and C bonds only to G. This arrangement of two nucleotides joined together across the double helix is called a base pair .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules.^ The strands of the DNA molecule are made-up of two molecules, the sugar and the phosphate molecules.
  • Dynamic model of the DNA molecule - US Patent 6036497 Description 16 October 2009 6:06 UTC www.patentstorm.us [Source type: Reference]

^ Figure 1: The DNA molecule showing base pairing.
  • science tips 16 October 2009 6:06 UTC rpdp.net [Source type: Academic]

^ DNA - double helix .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

.These single-stranded DNA molecules have no single common shape, but some conformations are more stable than others.^ These are important times; more so than any other time in history.
  • DNA Activation Music - DNA Recoding - DNA Restranding - Activate Your DNA through Sound 19 January 2010 8:50 UTC www.activateyourdna.com [Source type: General]

^ Single-stranded DNA and repair of mutations .
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

^ These molecules have no single shape, but some conformations are more stable than others.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[18]

Sense and antisense

.A DNA sequence is called "sense" if its sequence is the same as that of a messenger RNA copy that is translated into protein.^ DNA is copied into RNA by RNA polymerases .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ A DNA sequence is called a "sense" sequence if it is copied by these enzymes (which only work in the 5' to 3' direction) and then translated into protein.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA polymerases copy DNA sequences.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.The sequence on the opposite strand is complementary to the sense sequence and is therefore called the "antisense" sequence.^ The sequence on the opposite strand is complementary to the sense sequence and is called the "antisense" sequence.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The two strands of DNA separate, and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Sense and antisense sequences can co-exist on the same strand of DNA; in both prokaryotes and eukaryotes, antisense sequences are transcribed [31] , and antisense RNAs might be involved in regulating gene expression.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

Since RNA polymerases work by making a complementary copy of their templates, it is this antisense strand that is the template for producing the sense messenger RNA. Both sense and antisense sequences can exist on different parts of the same strand of DNA (i.e. both strands contain both sense and antisense sequences). In both prokaryotes and eukaryotes, antisense RNA sequences are produced, but the functions of these RNAs are not entirely clear.[19] .One proposal is that antisense RNAs are involved in regulating gene expression through RNA-RNA base pairing.^ Regulation of gene expression .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The E2F and DP protein families form heterodimeric transcription factors that have a central role in the expression of cell-cycle-regulated genes and recognize a c/gGCGCg/c sequence.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ If the new gene regulates the first gene, it may be assigned the symbol of the first gene with the suffix “as” for antisense.
  • MGI-Guidelines for Nomenclature of Genes, Genetic Markers, Alleles, & Mutations in Mouse & Rat 16 January 2010 1:27 UTC www.informatics.jax.org [Source type: Academic]

[20]
.A few DNA sequences in prokaryotes and eukaryotes, and more in plasmids and viruses, blur the distinction made above between sense and antisense strands by having overlapping genes.^ The method of claim 2, wherein said double stranded DNA consists of the sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ A study examined 5 polymorphic Alu Chromosomal abnormalities in which a DNA sequences are inserted into genes, disrupting the normal structure and function of those genes.
  • DNA Evidence and Molecular Genetics Disprove the Book of Mormon 19 January 2010 18:22 UTC www.godandscience.org [Source type: Academic]

^ Preferably, the dsDNA epitopesare polynucleotides, said polynucleotide preferably comprising, consisting essentially of or consisting of the double stranded DNA sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[21] .In these cases, some DNA sequences do double duty, encoding one protein when read 5′ to 3′ along one strand, and a second protein when read in the opposite direction (still 5′ to 3′) along the other strand.^ DNA synthesis proceeds on both single strands in opposite directions.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ In a double helix, the direction of the nucleotides in one strand is opposite to that in the other strand.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ In these cases, some DNA sequences encode one protein when read from 5′ to 3′ along one strand, and a different protein when read in the opposite direction (but still from 5′ to 3′) along the other strand.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.In bacteria, this overlap may be involved in the regulation of gene transcription,[22] while in viruses, overlapping genes increase the amount of information that can be encoded within the small viral genome.^ In bacteria, this overlap may be involved in regulating gene transcription, [34] while in viruses , overlapping genes increase the information that can be encoded within the small viral genome.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Overlapping genes in vertebrate genomes .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Methylation of the CGG expansion results in decrease or silencing of FMR1 transcription and loss of the protein encoded by the gene (see Abnormal gene product ).
  • FMR1-Related Disorders -- GeneReviews -- NCBI Bookshelf 16 January 2010 1:27 UTC www.ncbi.nlm.nih.gov [Source type: Academic]

[23] .Another way of reducing genome size is seen in some viruses that contain linear or circular single-stranded DNA as their genetic material.^ Another way of reducing genome size is seen in some viruses that contain linear or circular single-stranded DNA. [36] .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Another study of ancient (10,000+ years old) Genetic material found in mitochondria, the organelles that generate energy for the cell.
  • DNA Evidence and Molecular Genetics Disprove the Book of Mormon 19 January 2010 18:22 UTC www.godandscience.org [Source type: Academic]

[24][25]

Supercoiling

.DNA can be twisted like a rope in a process called DNA supercoiling.^ DNA can be 'twisted' in a process called DNA supercoiling .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA is shaped like a twisted ladder.

^ The DNA molecule is first wound around special proteins called histones, just like a cotton reel.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

.With DNA in its "relaxed" state, a strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted the strands become more tightly or more loosely wound.^ In its "relaxed" state, a DNA strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted, the strands become more tightly or more loosely wound.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA double stranded state is actually its "resting state".

^ The double helix is itself twisted.

[26] .If the DNA is twisted in the direction of the helix, this is positive supercoiling, and the bases are held more tightly together.^ If the DNA is twisted in the direction of the helix (positive supercoiling), and the bases are held more tightly together.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The two strands of a DNA double helix are held together by ________.

^ Each strand of the DNA molecule is held together at its base by a weak bond.
  • DNA 101 19 January 2010 18:22 UTC blairdna.com [Source type: Academic]

.If they are twisted in the opposite direction, this is negative supercoiling, and the bases come apart more easily.^ If they are twisted in the opposite direction (negative supercoiling) the bases come apart more easily.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The conformation of a DNA molecule depends on its sequence, the amount and direction of supercoiling, chemical modifications of the bases, and also solution conditions, such as the concentration of metal ions.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ A DNA segment with excess or insufficient helical twisting is referred to, respectively, as positively or negatively "supercoiled".
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

.In nature, most DNA has slight negative supercoiling that is introduced by enzymes called topoisomerases.^ DNA can be 'twisted' in a process called DNA supercoiling .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Most DNA has slight negative supercoiling that is introduced by topoisomerases .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ In nature, these enzymes protect bacteria against phage infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the restriction modification system .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[27] .These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as transcription and DNA replication.^ Topoisomerases I promote the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of DNA replication, transcription and recombination.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ During DNA Recoding, you will find fairly high levels of excreted proteins in body fluids such as urine.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ Two ß strands protrude from the barrel, one of which extends into the DNA major groove.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[28]
From left to right, the structures of A, B and Z DNA

Alternative double-helical structures

.DNA exists in several possible conformations.^ Accordingly, DNA can exist in several possible conformations, but only a few of these ("A-DNA", "B-DNA", and "Z-DNA") are thought to occur naturally.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

The conformations so far identified are: A-DNA, B-DNA, C-DNA, D-DNA,[29] E-DNA,[30] H-DNA,[31] L-DNA,[29] P-DNA,[32] and Z-DNA.[8][33] .However, only A-DNA, B-DNA, and Z-DNA have been observed in naturally occurring biological systems.^ In particular, epitopes of interest include those that bind the anti-polynucleotide(particularly anti-double stranded DNA) antibodies that occur in systemic lupus erythematosis.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ In nature, these enzymes protect bacteria against phage infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the restriction modification system .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Accordingly, DNA can exist in several possible conformations, but only a few of these ("A-DNA", "B-DNA", and "Z-DNA") are thought to occur naturally.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.Which conformation DNA adopts depends on the sequence of the DNA, the amount and direction of supercoiling, chemical modifications of the bases and also solution conditions, such as the concentration of metal ions and polyamines.^ Preferably, the polynucleotide is DNA. As used herein, "DNA" includes not only bases A, T, C, and G, but also includes any of their analogs or modified forms of these bases, such as methylated nucleotides, internucleotide modifications such asuncharged linkages and thioates, use of sugar analogs, and modified and/or alternative backbone structures, such as polyamides.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The flanking domain, which includes a helix that projects into the major groove and an extended chain that travels along the minor groove, makes all of the sequence-determining contacts with the DNA. The core domain makes no direct contacts with the DNA bases.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ This approach is not new, but in the past researchers have concentrated on only 7&percent; of the total mitochondrial DNA sequence, known as the control regions.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

[34] .Of these three conformations, the "B" form described above is most common under the conditions found in cells.^ Player Pianos The player piano was the most common automatic musical instrument in use in the first three decades of the 20th century and could be found in thousands of private homes.

^ Nearly every cell in a person’s body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA).

^ In the complex cells that make up plants, animals and in other multi-celled organisms, most of the DNA is found in the chromosomes , which are located in the cell nucleus .

[35] .The two alternative double-helical forms of DNA differ in their geometry and dimensions.^ Dynamics of the B-A transition of DNA double helices.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

^ Helical Parameters of the three forms of DNA .
  • DNA - Proteopedia, life in 3D 19 January 2010 18:22 UTC www.proteopedia.org [Source type: Academic]

^ The two other known double-helical forms of DNA, called A and Z, differ modestly in their geometry and dimensions .
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

.The A form is a wider right-handed spiral, with a shallow and wide minor groove and a narrower and deeper major groove.^ The A form is a wider right-handed spiral, with a shallow and wide minor groove and a narrower and deeper major groove; this form occurs in dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The double helix is a right-handed spiral.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Two of these grooves twist around the surface of the double helix: the major groove is 22 Å wide and the minor groove is 12 Å wide.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.The A form occurs under non-physiological conditions in dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes.^ The A form appears likely to occur only in dehydrated samples of DNA, such those used in crystallography experiments, and possibly in hybrid pairings of DNA and RNA strands.
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

^ The A form is a wider right-handed spiral, with a shallow and wide minor groove and a narrower and deeper major groove; this form occurs in dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ RNA which goes on to produce the protein/enzyme.
  • The DNA double helix must unwind and separate into two strands so that one strand can assemble the proper 20 September 2009 11:58 UTC askville.amazon.com [Source type: General]

[36][37] .Segments of DNA where the bases have been chemically-modified by methylation may undergo a larger change in conformation and adopt the Z form.^ Segments of DNA where the bases have been modified by methylation may undergo a larger change in conformation and adopt the Z form.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ DNA(Instructions)> RNA(Messenger)> Protein(Synthesis - 3000 gene base pairs may contain 1000 amino acids).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

.Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form.^ Read more about it here .
  • Lupine Nuncio - Gene Wolfe News and Rumors 16 January 2010 1:27 UTC mysite.verizon.net [Source type: General]

^ Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA is made of two ("duplex DNA") dextrogyre (like a screw; right-handed) helical chains or strands ("the double helix"), coiled around an axis to form a double helix of 20A° of diameter.

[38] .These unusual structures can be recognised by specific Z-DNA binding proteins and may be involved in the regulation of transcription.^ Dataset of protein-DNA complex structures .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ DNA-binding proteins .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in regulating transcription.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[39]
.
Structure of a DNA quadruplex formed by telomere repeats.
^ Quadruplex DNA: sequence, topology and structure .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ A DNA segment that includes the telomere repeat sequence (TTAGGG)n and which maps to a telomeric location is symbolized in four parts: .
  • MGI-Guidelines for Nomenclature of Genes, Genetic Markers, Alleles, & Mutations in Mouse & Rat 16 January 2010 1:27 UTC www.informatics.jax.org [Source type: Academic]

^ The structure forms a large cleft in which the DNA is bound with the major groove facing the strands [ 50 ].
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

The conformation of the DNA backbone diverges significantly from the typical helical structure[40]

Quadruplex structures

.At the ends of the linear chromosomes are specialized regions of DNA called telomeres.^ At the ends of the linear chromosomes, specialized regions called telomeres allow the cell to replicate chromosome ends using the enzyme telomerase .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Normal human chromosomes have long, G-rich telomeric overhangs at one end .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ In bacteria , there is no nuclear membrane around the DNA, which is in a region called the nucleoid .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.The main function of these regions is to allow the cell to replicate chromosome ends using the enzyme telomerase, as the enzymes that normally replicate DNA cannot copy the extreme 3′ ends of chromosomes.^ Proteins are fundamental components of all living cells and include many substances, such as enzymes, hormones, and antibodies, that are necessary for the proper functioning of an organism.

^ Telomeres are nucleoprotein complexes found at the ends of eukaryotic chromosomes where the DNA consists of a repeated array of short, species-specific sequence motifs.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Many enzymes have to exist alongside DNA during replication and protein synthesis.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

[41] .As a result, if a chromosome lacked telomeres it would become shorter each time it was replicated.^ Without telomeres, a chromosome would become shorter each time it was replicated.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Telomere is the end of a chromosome, which consists of repeated sequences of DNA that perform the function of ensuring that each cycle of DNA replication has been completed.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ At the ends of the linear chromosomes, specialized regions called telomeres allow the cell to replicate chromosome ends using the enzyme telomerase .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.These specialized chromosome caps also help protect the DNA ends from exonucleases and stop the DNA repair systems in the cell from treating them as damage to be corrected.^ These nucleosomes are specially designed to protect the DNA and stop it being damaged.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ Telomere is the end of a chromosome, which consists of repeated sequences of DNA that perform the function of ensuring that each cycle of DNA replication has been completed.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

^ But each cell also contains structures called mitochondria, and these house DNA that is independent of that found in chromosomes.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

[42] .In human cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence.^ Single-stranded DNA and repair of mutations .
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

^ Structure and stability of human telomeric sequence.
  • Chemical Reagents for Investigating the Major Groove of DNA | Current Protocols 20 November 2009 8:55 UTC www.currentprotocols.com [Source type: Academic]

^ Single-stranded DNA .

[43]
.These guanine-rich sequences may stabilize chromosome ends by forming very unusual structures of stacked sets of four-base units, rather than the usual base pairs found in other DNA molecules.^ These sequences may stabilize chromosome ends by forming unusual quadruplex structures.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA information is carried by four bases.

^ In its "relaxed" state, a DNA strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted, the strands become more tightly or more loosely wound.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.Here, four guanine bases form a flat plate and these flat four-base units then stack on top of each other, to form a stable G-quadruplex structure.^ Here, four guanine bases form a flat plate, through hydrogen bonding , and these plates then stack on top of each other to form a stable quadruplex.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Preferably, the polynucleotide is DNA. As used herein, "DNA" includes not only bases A, T, C, and G, but also includes any of their analogs or modified forms of these bases, such as methylated nucleotides, internucleotide modifications such asuncharged linkages and thioates, use of sugar analogs, and modified and/or alternative backbone structures, such as polyamides.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Because of the chemical nature of these bases, adenine always pairs with thymine and guanine always pairs with cytosine.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[44] .These structures are stabilized by hydrogen bonding between the edges of the bases and chelation of a metal ion in the centre of each four-base unit.^ Helicases are a type of ' molecular motor '; they use the chemical energy in nucleoside triphosphates (predominantly ATP ) to break hydrogen bonds between bases and unwind the DNA double helix into single strands.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The double helix is held together by hydrogen bonds between the bases attached to the two strands.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The conformation of a DNA molecule depends on its sequence, the amount and direction of supercoiling, chemical modifications of the bases, and also solution conditions, such as the concentration of metal ions.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.The structure shown to the left is a top view of the quadruplex formed by a DNA sequence found in human telomere repeats.^ Telomeres are nucleoprotein complexes found at the ends of eukaryotic chromosomes where the DNA consists of a repeated array of short, species-specific sequence motifs.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The DNA-binding motif is found in many transcription regulators and more than a thousand distinct motifs have been identified through sequence analysis [ 26 ].
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ This review provides a general overview of the DNA-binding structures that have been found, along with detailed descriptions of the individual protein families.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.The single DNA strand forms a loop, with the sets of four bases stacking in a central quadruplex three plates deep.^ DNA information is carried by four bases.

^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The DNA-binding region of the Tus family is made of four antiparallel ß strands (colored red in Figure 6b ) which links the amino- and carboxy-terminal domains and produces a large central cleft in the protein.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.In the space at the centre of the stacked bases are three chelated potassium ions.^ Three aromatic residues from one helix intercalate into the major groove of the DNA to strikingly deform the base pair stacking (Figure 8h ).
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[45] .Other structures can also be formed, with the central set of four bases coming from either a single strand folded around the bases, or several different parallel strands, each contributing one base to the central structure.^ Other structures can also be formed, and the central set of four bases can come from either one folded strand, or several different parallel strands, each contributing one base to the central structure.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Definition: The basic structural unit of DNA. Context: Each strand of a DNA molecule is a linear arrangement of nucleotides, which are each composed of one sugar, one phosphate, and one nitrogenous base.

^ In 1953, James Watson and Francis Crick determined that the structure of DNA is a double-helix polymer, a spiral consisting of two DNA strands wound around each other.
  • DNA (chemical compound) -- Britannica Online Encyclopedia 19 January 2010 18:22 UTC www.britannica.com [Source type: Academic]

.In addition to these stacked structures, telomeres also form large loop structures called telomere loops, or T-loops.^ Lymph node A structure the size of a bean that contains large numbers of lymphocytes and is connected to other lymph nodes by small channels called lymphatics.
  • Leukemia & Lymphoma Society - Disease Page Definitions 16 January 2010 1:27 UTC www.leukemia-lymphoma.org [Source type: Academic]

^ These proteins seem to stabilize single-stranded DNA and protect it from forming stem loops or being degraded by nucleases .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The presence in Mfd of the highly conserved TRG motif forming the helical hairpin and adjacent loop structures in RecG suggests that these two enzymes may have very similar translocation motors derived from a common ancestor.
  • A model for dsDNA translocation revealed by a structural motif common to RecG and Mfd proteins : Article : The EMBO Journal 20 September 2009 12:012 UTC www.nature.com [Source type: Academic]

.Here, the single-stranded DNA curls around in a long circle stabilized by telomere-binding proteins.^ Single-stranded DNA and repair of mutations .
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

^ DNA-binding proteins .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA binding proteins .

[46] .At the very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands.^ Single-stranded DNA and repair of mutations .
  • fUSION Anomaly. DNA 19 January 2010 18:22 UTC fusionanomaly.net [Source type: Academic]

^ Two strands of DNA are held together in the shape of a double helix by the bonds between base pairs.

^ Dynamics of the B-A transition of DNA double helices.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

This triple-stranded structure is called a displacement loop or D-loop.[44]

Chemical modifications

cytosine 5-methylcytosine thymine
Structure of cytosine with and without the 5-methyl group. After deamination the 5-methylcytosine has the same structure as thymine

Base modifications

The expression of genes is influenced by the chromatin structure of a chromosome and regions of heterochromatin (low or no gene expression) correlate with the methylation of cytosine. .For example, cytosine methylation, to produce 5-methylcytosine, is important for X-chromosome inactivation.^ For example, cytosine methylation, to produce 5-methylcytosine , is important for X-chromosome inactivation .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The expression of genes is influenced by the chromatin structure of a chromosome, and regions of heterochromatin (with little or no gene expression) correlate with the methylation of cytosine .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Despite the biological importance of 5-methylcytosine, it is susceptible to spontaneous deamination , and methylated cytosines are therefore mutation 'hotspots'.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[47] .The average level of methylation varies between organisms, with Caenorhabditis elegans lacking cytosine methylation, while vertebrates show higher levels, with up to 1% of their DNA containing 5-methylcytosine.^ The level of methylation varies between organisms; the nematode C. elegans lacks any cytosine methylation, while up to 1% of the DNA of vertebrates contains 5-methylcytosine.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ For example, cytosine methylation, to produce 5-methylcytosine , is important for X-chromosome inactivation .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[48] .Despite the biological role of 5-methylcytosine it is susceptible to spontaneous deamination to leave the thymine base, and methylated cytosines are therefore mutation hotspots.^ Each DNA is a double stranded helix where the strands are linked by hydrogen bonds (Base Pairs) between guamine & cytosine, thymine & adenine.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ Each DNA has a set of nucleotides(Phosphate, Sugar(deoxyribose), Base(gaunine, cytosine), Nitrogen(Thymine, Ardenine).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

[49] .Other base modifications include adenine methylation in bacteria and the glycosylation of uracil to produce the "J-base" in kinetoplastids.^ Preferably, the polynucleotide is DNA. As used herein, "DNA" includes not only bases A, T, C, and G, but also includes any of their analogs or modified forms of these bases, such as methylated nucleotides, internucleotide modifications such asuncharged linkages and thioates, use of sugar analogs, and modified and/or alternative backbone structures, such as polyamides.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[50][51]

DNA damage

Benzopyrene, the major mutagen in tobacco smoke, in an adduct to DNA.[52]
DNA can be damaged by many different sorts of mutagens. .These include oxidizing agents, alkylating agents and also high-energy electromagnetic radiation such as ultraviolet light and x-rays.^ Examples of mutagens include oxidizing agents , alkylating agents and high-energy electromagnetic radiation such as ultraviolet light and x-rays .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.The type of DNA damage produced depends on the type of mutagen.^ "Bipyrimidine photoproducts rather than oxidative lesions are the main type of DNA damage involved in the genotoxic effect of solar ultraviolet radiation".
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ SOS induction could not elicit iSDR Homologous recombination-dependent initiation of DNA replication from DNA damage-inducible origins in Escherichia coli.
  • WikiGenes - recA - DNA strand exchange and recombination... 19 November 2009 18:56 UTC www.wikigenes.org [Source type: Academic]

^ Mutagens are agents which can produce genetic mutations - these are alterations of one DNA base to another base.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.For example, UV light mostly damages DNA by producing thymine dimers, which are cross-links between adjacent pyrimidine bases in a DNA strand.^ "Hydroxyl radicals and DNA base damage".
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Ultraviolet radiation damages DNA mostly by producing thymine dimers .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[53] .On the other hand, oxidants such as free radicals or hydrogen peroxide produce multiple forms of damage, including base modifications, particularly of guanosine, as well as double-strand breaks.^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ A "double-stranded DNA epitope" or "dsDNA epitope" is any chemical moiety which exhibits specific binding to an anti-double-stranded DNA antibody and as such includes molecules which comprise such epitope(s).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Usually the linker containing strand of the duplex is coupled at or proximate (i.e., within about 5 base pairs) to one of its ends such that each strand forms a pendant chainof at least about 20 base pairs measured from the site of attachment of the strand to the linker molecule.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[54] .It has been estimated that in each human cell, about 500 bases suffer oxidative damage per day.^ Based on our observations, the amount sufficient for this reduction for LJP 394 is about 100 mg,given once per week.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ For purposes of this invention, a polynucleotide is generally an isolated polynucleotide of less than about 1 kb, preferably less than about 500 base pairs (bp), preferably less than about250 bp, preferably less than about 100 bp, preferably less than about 50 bp.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The scientists then chopped the entire DNA of a human cell into pieces of about the same length and mixed them with the message strand.

[55][56] .Of these oxidative lesions, the most dangerous are double-strand breaks, as these lesions are difficult to repair and can produce point mutations, insertions and deletions from the DNA sequence, as well as chromosomal translocations.^ "The role of double-strand break repair - insights from human genetics".
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Of these lesions, the most damaging are double-strand breaks, as they can produce point mutations , insertions and deletions from the DNA sequence, as well as chromosomal translocations .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ "Regulation and mechanisms of mammalian double-strand break repair".
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[57]
.Many mutagens intercalate into the space between two adjacent base pairs.^ Many mutagens intercalate into the space between two adjacent base pairs.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ As the DNA strands wind around each other, gaps between the two phosphate backbones reveal the sides of the bases inside (see animation).
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Each DNA is a double stranded helix where the strands are linked by hydrogen bonds (Base Pairs) between guamine & cytosine, thymine & adenine.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

.Intercalators are mostly aromatic and planar molecules, and include ethidium, daunomycin, doxorubicin and thalidomide.^ These are mostly polycyclic, aromatic , and planar molecules, and include ethidium , proflavin , daunomycin , doxorubicin and thalidomide .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.In order for an intercalator to fit between base pairs, the bases must separate, distorting the DNA strands by unwinding of the double helix.^ Each DNA is a double stranded helix where the strands are linked by hydrogen bonds (Base Pairs) between guamine & cytosine, thymine & adenine.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ DNA - double helix .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

^ DNA double helix 7-038 .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

.These structural changes inhibit both transcription and DNA replication, causing toxicity and mutations.^ These structural modifications inhibit transcription and replication processes, causing both toxicity and mutations.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Nevertheless, because they can inhibit DNA transcription and replication, they are also used in chemotherapy to suppress rapidly-growing cancer cells.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Pabo CO, Sauer RT: Transcription factors: structural families and principles of DNA recognition.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.As a result, DNA intercalators are often carcinogens, with benzopyrene diol epoxide, acridines, aflatoxin and ethidium bromide being well-known examples.^ The kink results from the intercalation of specific hydrophobic side chains into the DNA structure, but without causing any significant distortion of the protein structure relative to the uncomplexed protein in solution.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The resulting structure often has a U-shaped cavity in which the DNA is bound [ 56 ] and often the DNA structure is severely deformed on binding.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Often the 12 strands of DNA are more associated with higher beings, higher dimensions, and the spirit.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

[58][59][60] .Nevertheless, due to their properties of inhibiting DNA transcription and replication, they are also used in chemotherapy to inhibit rapidly-growing cancer cells.^ Nevertheless, because they can inhibit DNA transcription and replication, they are also used in chemotherapy to suppress rapidly-growing cancer cells.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA intercalators are used in chemotherapy to inhibit DNA replication in rapidly-growing cancer cells.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ These structural modifications inhibit transcription and replication processes, causing both toxicity and mutations.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[61]

Overview of biological functions

DNA usually occurs as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. .The set of chromosomes in a cell makes up its genome; the human genome has approximately 3 billion base pairs of DNA arranged into 46 chromosomes.^ There are 3 billion base pairs in the human genome.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ Inside every human cell are 23 pairs of chromosomes, made up of DNA .
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ DNA(Instructions)> RNA(Messenger)> Protein(Synthesis - 3000 gene base pairs may contain 1000 amino acids).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

[62] .The information carried by DNA is held in the sequence of pieces of DNA called genes.^ DNA information is carried by four bases.

.Transmission of genetic information in genes is achieved via complementary base pairing.^ DNA(Instructions)> RNA(Messenger)> Protein(Synthesis - 3000 gene base pairs may contain 1000 amino acids).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ A gene has about one thousand to several million base pairs.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

.For example, in transcription, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence through the attraction between the DNA and the correct RNA nucleotides.^ DNA polymerases copy DNA sequences.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA is copied into RNA by RNA polymerases .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Some DNA sequences encode important information for the cell.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

.Usually, this RNA copy is then used to make a matching protein sequence in a process called translation which depends on the same interaction between RNA nucleotides.^ The pairwise sequence identities between the subunits in the Cro and Repressor family range from 68% (1lmbA and 1perA) to 100% for identical proteins (1lliA and 1lmbA).
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The program uses a dynamic programming method [ 9 ] and assesses the similarity between proteins by comparing the structural environments of the constituent amino acids.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ As our main research interest lies in the investigation of interactions between proteins and DNA, the main focus is on X-ray structures of complexes that provide the requisite details.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.Alternatively, a cell may simply copy its genetic information in a process called DNA replication.^ DNA can be 'twisted' in a process called DNA supercoiling .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ When cells divide, the genetic information must be duplicated to produce two daughter copies of DNA in a process called DNA replication .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The DNA contains the genetic information of the cell.
  • DNA Intuitive Healings 19 January 2010 8:50 UTC www.selacia.com [Source type: FILTERED WITH BAYES]

.The details of these functions are covered in other articles; here we focus on the interactions between DNA and other molecules that mediate the function of the genome.^ There are many interactions that happen between DNA and other molecules to coordinate its functions.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ "Genomic DNA methylation: the mark and its mediators".
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ This topic has been covered in detail elsewhere on this website so there is no reason to repeat the information here.

Genome structure

.Genomic DNA is located in the cell nucleus of eukaryotes, as well as small amounts in mitochondria and chloroplasts.^ But each cell also contains structures called mitochondria, and these house DNA that is independent of that found in chromosomes.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ Examination of genes that are functionally assigned in PEDANT [ 3 ] show that typically 2-3% of a prokaryotic genome and 6-7% of a eukaryotic genome encodes DNA-binding proteins.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Each cell has a nucleus(23 chromosomes(Coiled threads of DNA Helix molecules+Protein molecules).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

.In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid.^ DNA's entrance within the human body is via the light receptor which is the Pineal Gland, the single eye.

^ That external DNA or God factor which enters within the body to develop healing is the result of light interacting with Green.

[63] The genetic information in a genome is held within genes. .A gene is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism.^ Line 1: DNA is is the principal constituent of Genes, the structures that transmit hereditary characteristics.

Genes contain an open reading frame that can be transcribed, as well as regulatory sequences such as promoters and enhancers, which control the expression of the open reading frame.
.In many species, only a small fraction of the total sequence of the genome encodes protein.^ This approach is not new, but in the past researchers have concentrated on only 7&percent; of the total mitochondrial DNA sequence, known as the control regions.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

.For example, only about 1.5% of the human genome consists of protein-coding exons, with over 50% of human DNA consisting of non-coding repetitive sequences.^ The following are non-limiting examples of polynucleotides: a gene or gene fragment, exons, introns, mRNA, tRNA, rRNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence,isolated RNA of any sequence, nucleic acid probes, and primers.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The method of claim 2, wherein said double stranded DNA consists of the sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ As shown in Figure 3a , each subunit in the leucine zipper protein consists of a single a helix about 60 amino acids long.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[64] The reasons for the presence of so much non-coding DNA in eukaryotic genomes and the extraordinary differences in genome size, or C-value, among species represent a long-standing puzzle known as the "C-value enigma."[65] However, DNA sequences that do not code protein may still encode functional non-coding RNA molecules, which are involved in the regulation of gene expression.[66]
.
T7 RNA polymerase (blue) producing a mRNA (green) from a DNA template (orange).
^ DNA polymerase T7 (pol T7) .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ DNA polymerases synthesize DNA strands by catalyzing the stepwise addition of a deoxyribonuleotide to the 3'-OH end of a polynucleotide chain that is paired to a second, template stand.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ T7 DNA polymerase (Figure 8k ) possesses no 5'-3'-exonuclease activity.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[67]
.Some non-coding DNA sequences play structural roles in chromosomes.^ Some non-coding DNA sequences are now known to have a structural role in chromosomes.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Quadruplex DNA: sequence, topology and structure .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ A study examined 5 polymorphic Alu Chromosomal abnormalities in which a DNA sequences are inserted into genes, disrupting the normal structure and function of those genes.
  • DNA Evidence and Molecular Genetics Disprove the Book of Mormon 19 January 2010 18:22 UTC www.godandscience.org [Source type: Academic]

.Telomeres and centromeres typically contain few genes, but are important for the function and stability of chromosomes.^ Examination of genes that are functionally assigned in PEDANT [ 3 ] show that typically 2-3% of a prokaryotic genome and 6-7% of a eukaryotic genome encodes DNA-binding proteins.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[42][68] .An abundant form of non-coding DNA in humans are pseudogenes, which are copies of genes that have been disabled by mutation.^ Two copies of each of four histone proteins are assembled into an octamer that has 145-147 bp of DNA wrapped in a superhelix around it to form a nucleosome core.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ DNA coded matrix which was designed to interface with the physical as well as non-physical domains ...
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ Scientists have devised a way of hiding a coded message in a dot of human DNA. .

[69] .These sequences are usually just molecular fossils, although they can occasionally serve as raw genetic material for the creation of new genes through the process of gene duplication and divergence.^ The article says that investors are starting to scramble to get in on the the coming new technology of spelling out the precise sequence of the three billion letters in the human genetic code.

^ Continuing the genetic engineering, they created 14 more, 7 male and 7 female.
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ Jehovah thought that they got the wrong end of the genetic make up of Abraham and that the Ishmael got the smart-genes.....
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

[70]

Transcription and translation

.A gene is a sequence of DNA that contains genetic information and can influence the phenotype of an organism.^ DNA(Instructions)> RNA(Messenger)> Protein(Synthesis - 3000 gene base pairs may contain 1000 amino acids).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ The encyclopedia goes on, " The complementarity of this bonding insures that DNA can be replicated, that identical copies can be made in order to transmit genetic information to the next generation.

^ The protein 3hts (Figure 1o ) recognizes the promoters of the heat-shock protein genes through upstream DNA sequences (heat-shock elements, HSEs).
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.Within a gene, the sequence of bases along a DNA strand defines a messenger RNA sequence, which then defines one or more protein sequences.^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ DNA(Instructions)> RNA(Messenger)> Protein(Synthesis - 3000 gene base pairs may contain 1000 amino acids).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ The method of claim 2, wherein said double stranded DNA consists of the sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

.The relationship between the nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the rules of translation, known collectively as the genetic code.^ DNA(Instructions)> RNA(Messenger)> Protein(Synthesis - 3000 gene base pairs may contain 1000 amino acids).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ As shown in Figure 3a , each subunit in the leucine zipper protein consists of a single a helix about 60 amino acids long.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The E2F and DP protein families form heterodimeric transcription factors that have a central role in the expression of cell-cycle-regulated genes and recognize a c/gGCGCg/c sequence.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.The genetic code consists of three-letter 'words' called codons formed from a sequence of three nucleotides (e.g.^ These 3 base sequences are called codons.
  • science tips 20 September 2009 11:58 UTC www.rpdp.net [Source type: FILTERED WITH BAYES]

^ The genetic code consists of three-letter 'words' called codons formed from a sequence of three nucleotides.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The only reason for these potentially very threatening diseases is that one or a few of the millions of letters in the genetic code are in the wrong place.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

ACT, CAG, TTT).
.In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase.^ DNA(Instructions)> RNA(Messenger)> Protein(Synthesis - 3000 gene base pairs may contain 1000 amino acids).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ But unknowns to you there are things called parasitic genes that reproduce by inserting copies of themselves into new locations in the chromosomes.

^ TATA box-binding proteins are an essential component of the multiprotein transcription initiator complex that assembles on promoters bound by RNA polymerase II. .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.This RNA copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the messenger RNA to transfer RNA, which carries amino acids.^ DNA(Instructions)> RNA(Messenger)> Protein(Synthesis - 3000 gene base pairs may contain 1000 amino acids).
  • DNA - PAST AND FUTURE 19 January 2010 18:22 UTC www.greatdreams.com [Source type: Original source]

^ Amino acids at positions -1, 2, 3 and 6 relative to the start of the a helix are used to interact with the bases, -1 being the position that precedes the helix [ 27 , 28 ].
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequences of two proteins.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.Since there are 4 bases in 3-letter combinations, there are 64 possible codons (math combinations).^ As there are four bases in three-letter combinations, there are 64 possible codons, and these encode the twenty standard amino acids .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Since there are four different possibilities for each base of a codon, the total number of DNA codons is 4 3 or 64.

^ Since each letter of a codon has four possible letters (A, U, C or G) there are 64 different codons (4 x 4 x 4 = 64).

.These encode the twenty standard amino acids, giving most amino acids more than one possible codon.^ Already there are at least 70,000 more children under 12 being raised in homes with one Jewish parent than with two Jewish parents."
  • Chatological Humor (Updated 11.8.07) - washingtonpost.com 16 January 2010 1:27 UTC www.washingtonpost.com [Source type: General]

^ The result is a total of 54 protein families of which 33 contain more than one PDB entry.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ As described herein, in some embodiments, more than one measurement is made, when change(if any) in affinity is assessed.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

.There are also three 'stop' or 'nonsense' codons signifying the end of the coding region; these are the TAA, TGA and TAG codons.^ Also, there are three stop codons that terminate polypeptide synthesis.
  • Nucleic Acids 19 January 2010 18:22 UTC www.cem.msu.edu [Source type: Academic]

^ There is one start codon (AUG) that also encodes for methionine ) and three 'stop' or 'nonsense' codons (UAA, UGA and UAG) that signify the end of the coding region.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The dashes at the beginning and end of the overall sequence shown indicate that there is more sequence available both upstream and downstream of the region shown.
  • DNA Testing: An Introduction for Non-Scientists 19 January 2010 18:22 UTC www.scientific.org [Source type: FILTERED WITH BAYES]

DNA replication. The double helix is unwound by a helicase and topoisomerase. .Next, one DNA polymerase produces the leading strand copy.^ Two ß strands protrude from the barrel, one of which extends into the DNA major groove.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Each subunit consists of a seven-strand antiparallel ß barrel; one opening of this barrel forms a dimer interface with the equivalent segment of the other subunit while the other end points towards the DNA. .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The IRF DNA-binding region has an a/ß architecture consisting of a cluster of three a helices flanked on one side by a mixed four-stranded ß sheet (Figure 1m ).
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.Another DNA polymerase binds to the lagging strand.^ The proteins bind the minor groove with the three-stranded ß sheet causing the DNA to kink severely.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ A "double-stranded DNA epitope" or "dsDNA epitope" is any chemical moiety which exhibits specific binding to an anti-double-stranded DNA antibody and as such includes molecules which comprise such epitope(s).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Damaged DNA binds to UDG near the carboxy-terminal end of its central four-stranded ß sheet.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

This enzyme makes discontinuous segments (called Okazaki fragments) before DNA ligase joins them together.

Replication

.Cell division is essential for an organism to grow, but when a cell divides it must replicate the DNA in its genome so that the two daughter cells have the same genetic information as their parent.^ The encyclopedia goes on, " The complementarity of this bonding insures that DNA can be replicated, that identical copies can be made in order to transmit genetic information to the next generation.

^ Yes, the friend said, and like DNA they replicate themselves to relay their information.

^ "When the cell replicates, the twin strands of the DNA helix begin to unzip and separate.

.The double-stranded structure of DNA provides a simple mechanism for DNA replication.^ The method of claim 2, wherein said double stranded DNA consists of the sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Freedman LP, Luisi BF: On the mechanism of DNA-binding by nuclear hormone receptors - a structural and functional perspective.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Table 1 provides a summary of the families and Table 2 lists the 240 structures of protein-DNA complexes in the database.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.Here, the two strands are separated and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase.^ DNA is the long two stranded chain.

^ The method of claim 2, wherein said double stranded DNA consists of the sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ In addition, a double-strandedpolynucleotide can be obtained from the single stranded polynucleotide product of chemical synthesis either by synthesizing the complementary strand and annealing the strands under appropriate conditions, or by synthesizing the complementary strand denovo using a DNA polymerase with an appropriate primer.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

.This enzyme makes the complementary strand by finding the correct base through complementary base pairing, and bonding it onto the original strand.^ These pairings also referred as complementary base pairs.
  • science tips 16 October 2009 6:06 UTC rpdp.net [Source type: Academic]

^ Francis Crick and James Watson, at Cambridge University, considered hydrogen bonded base pairing interactions, and arrived at a double stranded helical model that satisfied most of the known facts, and has been confirmed by subsequent findings.
  • Nucleic Acids 19 January 2010 18:22 UTC www.cem.msu.edu [Source type: Academic]

^ These interactions together induce breakage of Watson-Crick nucleotide base pairing hydrogen bonds, resulting in bending of the DNA, strand elongation and unwinding events similar to those described for helicases (15 ).
  • Molecular Dynamics Simulations 20 November 2009 8:55 UTC www.msi.umn.edu [Source type: Academic]

.As DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction, different mechanisms are used to copy the antiparallel strands of the double helix.^ DNA double helix 7-038 .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

^ In a double helix, the direction of the nucleotides in one strand is opposite to that in the other strand.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The double-stranded structure of DNA provides a simple mechanism for this replication.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

[71] In this way, the base on the old strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.

Interactions with proteins

.All the functions of DNA depend on interactions with proteins.^ Protein-DNA interaction .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

^ All of the functions of DNA depend on its interactions with proteins.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Protein-DNA interactions: a structural analysis.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

.These protein interactions can be non-specific, or the protein can bind specifically to a single DNA sequence.^ Protein-DNA interaction .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

^ DNA-binding proteins .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Outline of the families of DNA-binding proteins .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.Enzymes can also bind to DNA and of these, the polymerases that copy the DNA base sequence in transcription and DNA replication are particularly important.^ These 3 base sequences are called codons.
  • science tips 20 September 2009 11:58 UTC www.rpdp.net [Source type: FILTERED WITH BAYES]

^ When these two DNA strands with matching sequences lock up at the right place, the helix is formed and can only be pulled apart by DNA polymerase or if the DNA itself becomes badly damaged and no longer contains large sections of bases inside its phosphate/sugar walls.
  • The DNA double helix must unwind and separate into two strands so that one strand can assemble the proper 20 September 2009 11:58 UTC askville.amazon.com [Source type: General]

^ Not all of the DNA is transcribed into RNA. Transcription starts when the RNA polymerase finds a promoter sequence on one strand of the DNA. That promoter sequence can appear on either strand; neither strand is specifically designated as the sense strand for its entire length.
  • The DNA double helix must unwind and separate into two strands so that one strand can assemble the proper 20 September 2009 11:58 UTC askville.amazon.com [Source type: General]

DNA-binding proteins

Interaction of DNA with histones (shown in white, top). These proteins' basic amino acids (below left, blue) bind to the acidic phosphate groups on DNA (below right, red).
.Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions.^ Dataset of protein-DNA complex structures .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ DNA-binding proteins .
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Outline of the families of DNA-binding proteins .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.Within chromosomes, DNA is held in complexes with structural proteins.^ Dataset of protein-DNA complex structures .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Structural taxonomy and classification of protein-DNA complexes .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Protein-DNA interactions: a structural analysis.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

.These proteins organize the DNA into a compact structure called chromatin.^ Dataset of protein-DNA complex structures .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ DNA in chromatin is organized in arrays of nucleosomes.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ According to scientists at MCP Hahnemann University in Philadelphia the mutated gene alters part of an important structural protein inside the disk called collagen 9.

.In eukaryotes this structure involves DNA binding to a complex of small basic proteins called histones, while in prokaryotes multiple types of proteins are involved.^ Dataset of protein-DNA complex structures .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Structural taxonomy and classification of protein-DNA complexes .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Outline of the families of DNA-binding proteins .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[72][73] .The histones form a disk-shaped complex called a nucleosome, which contains two complete turns of double-stranded DNA wrapped around its surface.^ DNA is the long two stranded chain.

^ The method of claim 2, wherein said double stranded DNA consists of the sequence 5'-GTGTGTGTGTGTGTGTGTGT-3' (SEQ ID NO: 1).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ Jointly the domains form a clamp around the DNA, inserting a helices into both the major and minor grooves [ 45 ].
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.These non-specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence.^ The rest of the domain interacts with the DNA backbone.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Histone and HMG are multimeric proteins that bind DNA independent of base sequence.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

[74] .Chemical modifications of these basic amino acid residues include methylation, phosphorylation and acetylation.^ Preferably, the polynucleotide is DNA. As used herein, "DNA" includes not only bases A, T, C, and G, but also includes any of their analogs or modified forms of these bases, such as methylated nucleotides, internucleotide modifications such asuncharged linkages and thioates, use of sugar analogs, and modified and/or alternative backbone structures, such as polyamides.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ These amino acids are in turn translated from the complex array of nucleic acids in DNA. .

^ The segment, known as the zipper region, consists of leucine or a similar hydrophobic amino acid every eight residue positions - roughly every two turns of the a helix.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[75] .These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription.^ Suzuki M, Brenner SE, Gerstein MB, Yagi N: DNA recognition code of transcription factors.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The ability to bend DNA is not only limited to the enzymes, however; although not as severe, DNA bending is clearly also a common feature of complexes formed by transcription factors.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ As our main research interest lies in the investigation of interactions between proteins and DNA, the main focus is on X-ray structures of complexes that provide the requisite details.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[76] .Other non-specific DNA-binding proteins found in chromatin include the high-mobility group proteins, which bind preferentially to bent or distorted DNA.[77] These proteins are important in bending arrays of nucleosomes and arranging them into more complex chromatin structures.^ Dataset of protein-DNA complex structures .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Group IV, 'other a helix proteins'.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The DNA is bent towards the protein [ 40 ].
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[78]
.A distinct group of DNA-binding proteins are the single-stranded-DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication protein A is the best-characterised member of this family and is essential for most processes where the double helix is separated, including DNA replication, recombination and DNA repair.^ Group IV, 'other a helix proteins'.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Group IV: other a-helix proteins .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Group IV: Other a-helix proteins .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[79] .These binding proteins seem to stabilize single-stranded DNA and protect it from forming stem loops or being degraded by nucleases.^ Outline of the families of DNA-binding proteins .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The DNA-binding region of the Tus family is made of four antiparallel ß strands (colored red in Figure 6b ) which links the amino- and carboxy-terminal domains and produces a large central cleft in the protein.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

The lambda repressor helix-turn-helix transcription factor bound to its DNA target[80]
.In contrast, other proteins have evolved to specifically bind particular DNA sequences.^ Group VII, 'other DNA-binding proteins'.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Outline of the families of DNA-binding proteins .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ It is further understood that a different polynucleotide (for example, in terms of size and/or sequence) other than the one that is to be, was, or will be used in treatment, as long as both polynucleotides exhibit equivalent (or convertible)binding affinities to anti-ds DNA antibodies from an individual.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

.The most intensively studied of these are the various classes of transcription factors, which are proteins that regulate transcription.^ The E2F and DP protein families form heterodimeric transcription factors that have a central role in the expression of cell-cycle-regulated genes and recognize a c/gGCGCg/c sequence.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The family of interferon regulatory factor (IRF) transcription factors is important in the regulation of inter-ferons in response to infection by virus and in the regulation of interferon-inducible genes.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ It is a transcriptional regulator of galactose-induced genes and its zinc-coordinating motif has so far only been identified in proteins from Saccharomyces cerevisiae .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.Each one of these proteins bind to one particular set of DNA sequences and thereby activates or inhibits the transcription of genes with these sequences close to their promoters.^ Outline of the families of DNA-binding proteins .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ It is further understood that a different polynucleotide (for example, in terms of size and/or sequence) other than the one that is to be, was, or will be used in treatment, as long as both polynucleotides exhibit equivalent (or convertible)binding affinities to anti-ds DNA antibodies from an individual.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The protein also binds DNA in the minor groove at a downstream site using the amino terminus of a helix to contact the DNA backbone.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.The transcription factors do this in two ways.^ Transcription factors do this in two ways.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

.Firstly, they can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription.^ Some can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The sigma subunit conveys promoter specificity to RNA polymerase ; that is, it is responsible for telling RNA polymerase where to bind.
  • DNA Transcription | Learn Science at Scitable 19 January 2010 18:22 UTC www.nature.com [Source type: Academic]

^ Transcription begins when the enzyme RNA polymerase attaches to the promoter.

[81] .Alternatively, transcription factors can bind enzymes that modify the histones at the promoter; this will change the accessibility of the DNA template to the polymerase.^ Suzuki M, Brenner SE, Gerstein MB, Yagi N: DNA recognition code of transcription factors.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The ability to bend DNA is not only limited to the enzymes, however; although not as severe, DNA bending is clearly also a common feature of complexes formed by transcription factors.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The loop-sheet-helix zinc-binding motif is represented solely by the DNA-binding region of p53, a transcriptional activator implicated in tumor suppression [ 2 , 34 ].
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[82]
.As these DNA targets can occur throughout an organism's genome, changes in the activity of one type of transcription factor can affect thousands of genes.^ These DNA targets can occur throughout an organism's genome, so changes in the activity of one type of transcription factor in a given cell can affect the expression of many genes in that cell.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Polyploid organisms also have one genome.

^ When the DNA synthesis is complete, an error occurs in one nucleotide in a thousand.
  • The Miracle of Creation in DNA - Harun Yahya 19 January 2010 18:22 UTC www.harunyahya.com [Source type: FILTERED WITH BAYES]

[83] .Consequently, these proteins are often the targets of the signal transduction processes that mediate responses to environmental changes or cellular differentiation and development.^ Proteins that contain the region act as transcription regulators for genes commonly involved in cellular defense and differentiation.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ For example, in proteins such as Hha I methyltransferases and endonucleases, a single change in the target sequence can lead to over a million-fold reduction in binding affinity.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The helix-loop-helix proteins are transcription factors that control the expression of a wide range of genes involved in differentiation and development.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to "read" the DNA sequence.^ The edges of the bases are more accessible in the major groove, so proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Protein-DNA interaction .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

^ Scientists reading DNA sequence .
  • Dna Stock Photos and Images. 2038 Dna pictures and royalty free photography available to search from over 100 stock photo brands. 19 November 2009 18:56 UTC www.fotosearch.com [Source type: General]

.Most of these base-interactions are made in the major groove, where the bases are most accessible.^ Most of these interactions occur in the major groove, where the bases are most accessible.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ The control simulation does not display a decrease in overall solvent-accessible area, the minor groove does not increase in area, and the major groove compresses minimally.
  • The B- to A-DNA Transition and the Reorganization of Solvent at the DNA Surface - Science News - redOrbit 20 November 2009 8:55 UTC www.redorbit.com [Source type: Academic]

^ These backbone interactions are reported to contribute to the protein's DNA binding affinity and to position the DNA recognition helices within their cognate operator DNA major groove halfsites (1 ).
  • Molecular Dynamics Simulations 20 November 2009 8:55 UTC www.msi.umn.edu [Source type: Academic]

[84]
The restriction enzyme EcoRV (green) in a complex with its substrate DNA[85]

DNA-modifying enzymes

Nucleases and ligases

.Nucleases are enzymes that cut DNA strands by catalyzing the hydrolysis of the phosphodiester bonds.^ When the intelligent enzymes find a distortion in the DNA the cut out the distorted part from one side of the helix and a small fragment of damaged DNA is released.

^ But what if the enzymes do not know how to repair a particular strand of DNA. It is not working properly and the enzymes cannot make the repair.

^ The enzymes are the ones that we saw who open up the defective DNA strand and make a way to correction or healing.

.Nucleases that hydrolyse nucleotides from the ends of DNA strands are called exonucleases, while endonucleases cut within strands.^ Each subunit consists of a ß barrel: one end of the barrel points towards the DNA and presents two ß strands, one of which extends into the major groove [ 51 ].
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Damaged DNA binds to UDG near the carboxy-terminal end of its central four-stranded ß sheet.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Each subunit consists of a seven-strand antiparallel ß barrel; one opening of this barrel forms a dimer interface with the equivalent segment of the other subunit while the other end points towards the DNA. .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.The most frequently-used nucleases in molecular biology are the restriction endonucleases, which cut DNA at specific sequences.^ The primary sequence-specific contacts made to homing-site DNA are from residues in the second ß sheet of each enzyme monomer which contact the major groove of each half-site.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ In prokaryotes the reaction is most commonly found in the protection of the DNA from restriction enzymes.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Telomeres are nucleoprotein complexes found at the ends of eukaryotic chromosomes where the DNA consists of a repeated array of short, species-specific sequence motifs.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.For instance, the EcoRV enzyme shown to the left recognizes the 6-base sequence 5′-GAT|ATC-3′ and makes a cut at the vertical line.^ For instance, the EcoRV enzyme recognizes the 6-base sequence 5′-GAT|ATC-3′ and makes a cut at the vertical line.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Endonuclease Fok I is a bipartite restriction enzyme which recognizes a specific DNA sequence and non-specifically cleaves at a position a short distance away.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ As noted in the 2'-deoxycytidine structure on the left, the numbering of the sugar carbons makes use of primed numbers to distinguish them from the heterocyclic base sites.
  • Nucleic Acids 19 January 2010 18:22 UTC www.cem.msu.edu [Source type: Academic]

.In nature, these enzymes protect bacteria against phage infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the restriction modification system.^ The polynucleotides may be isolated from the other DNA of the cell/microorganism by treatment with restriction enzymes andconventional size fractionation (e.g., agarose gel, Sephadex.TM. column).
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ The molecule also makes use of error checking strategies that ensure for example that the cell does not begin to read DNA in the middle of a sentence or skip part of an instruction."

[86] .In technology, these sequence-specific nucleases are used in molecular cloning and DNA fingerprinting.^ Polymerases must provide sequence-independent interactions with their DNA substrate, yet retain the specificity to distinguish correctly paired bases from mismatches.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ The primary sequence-specific contacts made to homing-site DNA are from residues in the second ß sheet of each enzyme monomer which contact the major groove of each half-site.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Telomeres are nucleoprotein complexes found at the ends of eukaryotic chromosomes where the DNA consists of a repeated array of short, species-specific sequence motifs.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

.Enzymes called DNA ligases can rejoin cut or broken DNA strands, using the energy from either adenosine triphosphate or nicotinamide adenine dinucleotide.^ When the intelligent enzymes find a distortion in the DNA the cut out the distorted part from one side of the helix and a small fragment of damaged DNA is released.

^ The term "circulating anti-double-stranded DNA antibody", as used herein, intends an anti-double-stranded DNA antibody which is not bound to a double-stranded DNA epitope on and/or in a biological sample, i.e., free antibody.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

^ But what if the enzymes do not know how to repair a particular strand of DNA. It is not working properly and the enzymes cannot make the repair.

[87] .Ligases are particularly important in lagging strand DNA replication, as they join together the short segments of DNA produced at the replication fork into a complete copy of the DNA template.^ Two ß strands protrude from the barrel, one of which extends into the DNA major groove.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Each subunit consists of a seven-strand antiparallel ß barrel; one opening of this barrel forms a dimer interface with the equivalent segment of the other subunit while the other end points towards the DNA. .
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ In particular, epitopes of interest include those that bind the anti-polynucleotide(particularly anti-double stranded DNA) antibodies that occur in systemic lupus erythematosis.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC www.patents.com [Source type: Academic]

.They are also used in DNA repair and genetic recombination.^ The ancients are not going to use the words science or DNA , they used symbols that meant science and DNA. .

^ Scientists report they have for the first time permanently repaired a genetic disease in animals.

[87]

Topoisomerases and helicases

Topoisomerases are enzymes with both nuclease and ligase activity. .These proteins change the amount of supercoiling in DNA. Some of these enzyme work by cutting the DNA helix and allowing one section to rotate, thereby reducing its level of supercoiling; the enzyme then seals the DNA break.^ While achieving a close fit between the a helix and major groove, there is enough flexibility to allow both the protein and DNA to adopt distinct conformations, resulting in multispecific complementarity.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ In contrast to many protein families, the a helix binds base and backbone groups from the DNA minor groove [ 51 ].
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

^ Unlike the proteins met with so far, the DNA-binding regions used by enzymes are generally hard to describe in terms of simple structural motifs, and these proteins use an extensive combination of a helices, ß strands and loops to recognize and bind DNA (Figure 8 ).
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[27] .Other types of these enzymes are capable of cutting one DNA helix and then passing a second strand of DNA through this break, before rejoining the helix.^ In a double helix, the direction of the nucleotides in one strand is opposite to that in the other strand.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Others can cut one DNA helix and then pass a second strand of DNA through this break, before rejoining the helix.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ Topoisomerase : This enzyme initiates unwinding of the double helix by cutting one of the strands.
  • Nucleic Acids 19 January 2010 18:22 UTC www.cem.msu.edu [Source type: Academic]

[88] .Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.^ Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.
  • DNA - encyclopedia article - Citizendium 19 January 2010 18:22 UTC en.citizendium.org [Source type: Academic]

^ DNA replication is bidirectional (There are two replication forks per circular DNA genome and replication involves leading/lagging strands, Okazaki fragments , DNA ligase , etc.

^ Topoisomerases I promote the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of DNA replication, transcription and recombination.
  • Genome Biology | Full text | An overview of the structures of protein-DNA complexes 20 November 2009 8:55 UTC genomebiology.com [Source type: Academic]

[28]
Helicases are proteins that are a type of molecular motor. .They use the chemical energy in nucleoside triphosphates, predominantly ATP, to break hydrogen bonds between bases and unwind the DNA double helix into single strands.^ The twin is DNA. The double helix.

^ These terms include a single-, double- or triple-stranded DNA,genomic DNA, cDNA, RNA, DNA-RNA hybrid, or a polymer comprising purine and pyrimidine bases, or other natural, chemically, biochemically modified, non-natural or derivatized nucleotide bases.
  • US 7081242 - Methods of treating lupus based on antibody affinity and screening methods and compositions for use thereof 20 September 2009 12:012 UTC