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<StructureSection load='B-DNA.pdb' size='540' frame='true' align='left' caption='B-DNA'  scene='DNA/B-dna/7'>
{{BAMBED
|DATE=August 20, 2011
|OLDID=1286497
|BAMBEDDOI=10.1002/bmb.20566
}}
<StructureSection load='B-DNA.pdb' size='450' side='right' scene='DNA/B-dna/7' caption='The double-helical structure of B-DNA, shown as ball-and-stick (colored by element {{Template:ColorKey_Element_C}} {{Template:ColorKey_Element_H}} {{Template:ColorKey_Element_O}} {{Template:ColorKey_Element_N}} {{Template:ColorKey_Element_P}}) with the helical conformation of the sugar-phosphate shown as orange ribbon, and the planes of the nucleobases (drag down in the viewer to see them) in orange as well.'>
 
'''Deoxyribonucleic acid''' or '''DNA'''  is a molecule which is the carrier of genetic information in nearly all the living organisms. It contains the biological instructions for the development, survival and reproduction of organisms.
'''Deoxyribonucleic acid''' or '''DNA'''  is a molecule which is the carrier of genetic information in nearly all the living organisms. It contains the biological instructions for the development, survival and reproduction of organisms.
DNA is found in the nucleus of a cell where it is packaged into a compact form called a chromosome with the help of several proteins known as histones. It is also found in cell structures called mitochondria. However in case of prokaryotes DNA is not enclosed in a nucleus or a membrane but is present in the cytoplasm. The DNA in prokaryotes in generally circular and supercoiled without any histones. DNA stores genetic information as a sequence of nucleotides in special regions known as genes which are used to make proteins. The expression of genetic information into proteins is a two-stage process wherein the sequence of nucleotides in DNA is converted to a molecule called Ribonucleic acid or [[RNA]] by a process called [[transcription]]. RNA is used to make proteins by another process called [[translation]]. The human genome contains nearly 3 · 10<sup>9</sup> bases with around 20,000 genes on 23 chromosomes. <ref name='gene'>http://www.genome.gov/25520880 </ref>  
DNA is found in the nucleus of a cell where it is packaged into a compact form called a chromosome with the help of several proteins known as histones. It is also found in cell structures called mitochondria. However in case of prokaryotes DNA is not enclosed in a nucleus or a membrane but is present in the cytoplasm. The DNA in prokaryotes in generally circular and supercoiled without any histones. DNA stores genetic information as a sequence of nucleotides in special regions known as genes which are used to make proteins. The expression of genetic information into proteins is a two-stage process wherein the sequence of nucleotides in DNA is converted to a molecule called Ribonucleic acid or [[RNA]] by a process called [[transcription]]. RNA is used to make proteins by another process called [[translation]]. The human genome contains nearly 3 · 10<sup>9</sup> bases with around 20,000 genes on 23 chromosomes. <ref name='gene'>http://www.genome.gov/25520880 </ref>  
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== Features of a DNA Molecule ==
== Features of a DNA Molecule ==
=== Double Helix ===
=== Double Helix ===
<scene name='User:Adithya_Sagar/Sandbox_DNA/B-dna/4'>DNA</scene> consists of two polynucleotide chains, <scene name='DNA/B-dna/16'>twisted around each other to form a double helix</scene>. The <scene name='DNA/Nucleotide/1'>nucleotide</scene> in DNA is composed of a <scene name='DNA/Phosphate/1'>phosphate</scene> bonded to the 5' of <scene name='DNA/Ribose/1'>D-2'-deoxyribose</scene> which is connected by a beta-glycosidic bond to a purine or a pyrimidine <scene name='DNA/Base/1'>base</scene>.  The four types of bases are the two double-ringed purine base <scene name='DNA/B-dna/22'>Adenine (A)</scene> and <scene name='DNA/B-dna/23'>Guanine (G)</scene> and the two single-ringed pyrimidine bases <scene name='DNA/B-dna/28'>Thymine (T)</scene> and <scene name='DNA/B-dna/27'>Cytosine (C)</scene>. Hydrogen atoms on some nitrogen and oxygen atom can undergo tautomeric shifts. The nitrogen atoms that are involved in forming tautomer appear as amino or imino groups and the oxygen atoms are either in keto or enol forms. Using an isolate thymine to illustrate the <scene name='DNA/Thymine_enol/1'>imino/enol tautomer</scene> and the <scene name='DNA/Thymine_keto/3'>amino/keto tautomer</scene>. There is a preference for the amino and keto forms which is very crucial for the biological functioning of DNA as it provides a <scene name='DNA/Amino-glycosidic/1'>ring nitrogen capable of forming a glycosidic bond</scene> with the deoxyribose and it leads to the specificity of hydrogen bonding in base pairing and thus complementarity of the chains.<ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref> The imino nitrogen can only serve as a donating atom in hydrogen bonding, but the amino nitrogen can also serve as a receiving atom. Each nucleotide in a DNA chain is linked to another via <scene name='DNA/Diester/2'>3',5' phosphodiester bond</scene>. There are four nucleotides in DNA.  The sugar-phosphate backbone of the DNA is very regular owing to the phosphodiester linkage whereas the ordering of bases is highly irregular.<ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref>
<scene name='User:Adithya_Sagar/Sandbox_DNA/B-dna/4'>DNA</scene> consists of two polynucleotide chains, <scene name='DNA/B-dna/16'>twisted around each other to form a double helix</scene>. The <scene name='10/100853/Nucleotide/2'>nucleotide</scene> in DNA is composed of a <scene name='10/100853/Phosphate/3'>phosphate</scene> bonded to the 5' of <scene name='10/100853/Deoxyribose/2'>D-2'-deoxyribose</scene> which is connected by a beta-glycosidic bond to a purine or a pyrimidine <scene name='10/100853/Base/2'>base</scene>. The <scene name='10/100853/Ribose_pucker/3'>ring pucker</scene> of ribose is a main determinant of which of the [[Forms of DNA]] is present. In this scene, which shows B DNA, the 2' carbon is out of the plane of the other members of the five membered ring.  In <scene name='10/100853/3_endo_a_dna/2'>A form DNA</scene>, the 3' carbon is out of the plane of the ribose ring.
The four types of bases are the two double-ringed purine base <scene name='10/100853/B-dna/38'>Adenine (A)</scene> and <scene name='10/100853/B-dna/39'>Guanine (G)</scene> and the two single-ringed pyrimidine bases <scene name='10/100853/B-dna/40'>Thymine (T)</scene> and <scene name='10/100853/B-dna/41'>Cytosine (C)</scene>. Hydrogen atoms on some nitrogen and oxygen atom can undergo tautomeric shifts. The nitrogen atoms that are involved in forming tautomer appear as amino or imino groups and the oxygen atoms are either in keto or enol forms. Using an isolate thymine to illustrate the <scene name='DNA/Thymine_enol/1'>imino/enol tautomer</scene> and the <scene name='DNA/Thymine_keto/3'>amino/keto tautomer</scene>. There is a preference for the amino and keto forms which is very crucial for the biological functioning of DNA as it provides a <scene name='10/100853/Amino-glycosidic/2'>ring nitrogen capable of forming a glycosidic bond</scene> with the deoxyribose and it leads to the specificity of hydrogen bonding in base pairing and thus complementarity of the chains.<ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref> The imino nitrogen can only serve as a donating atom in hydrogen bonding, but the amino nitrogen can also serve as a receiving atom. Each nucleotide in a DNA chain is linked to another via <scene name='10/100853/Diester/3'>3',5' phosphodiester bond</scene>. There are four nucleotides in DNA.  The sugar-phosphate backbone of the DNA is very regular owing to the phosphodiester linkage whereas the ordering of bases is highly irregular.<ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref>
<scene name='DNA/B-dna/17'>Restore View</scene>
<scene name='DNA/B-dna/17'>Restore View</scene>
{| class="wikitable" align= "center''
{| class="wikitable" align= "center''
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The two chains in a DNA are joined by hydrogen bonds between specific bases. Adenine forms base pairs with thymine and guanine with cytosine. This specific base pairing between <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/14'>Adenine-Thymine</scene> and <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/15'>Guanine-Cytosine</scene> is known as the Watson-Crick base pairing.  The specificity of hydrogen bonding between bases leads to complementarity in the sequence of nucleotides in the two chains.<ref name='structure'>A Structure for Deoxyribose Nucleic Acid
The two chains in a DNA are joined by hydrogen bonds between specific bases. Adenine forms base pairs with thymine and guanine with cytosine. This specific base pairing between <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/14'>Adenine-Thymine</scene> and <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/15'>Guanine-Cytosine</scene> is known as the Watson-Crick base pairing.  The specificity of hydrogen bonding between bases leads to complementarity in the sequence of nucleotides in the two chains.<ref name='structure'>A Structure for Deoxyribose Nucleic Acid
Watson J.D. and Crick F.H.C.
Watson J.D. and Crick F.H.C.
Nature 171, 737-738 (1953)</ref> Thus in a strand of DNA the content of adenine is equal to that of thymine  and the guanine content is equal to the cytosine content.  In general DNA with higher GC content is more stable than the one with higher AT content owing to the stabilization due to base stacking interactions.
Nature 171, 737-738 (1953)</ref> Thus in a strand of DNA the content of adenine is equal to that of thymine  and the guanine content is equal to the cytosine content.  In general DNA with higher GC content is more stable than the one with higher AT content owing to the stabilization due to [[base stacking]] interactions.


=== DNA denaturation and renaturation ===
=== DNA denaturation and renaturation ===
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=== Grooves ===
=== Grooves ===
In a <scene name='DNA/Bdnasf/1'>DNA double helix</scene> the <scene name='DNA/Angled_gylcosidic/5'>beta-glycosyl bonds</scene> of bases which are paired <scene name='DNA/Angled_gylcosidic/6'>do not lie opposite</scene> to each other but are positioned at an angle. This results in unequally spaced sugar-phosphate backbones and gives rise to two grooves: the
In a <scene name='DNA/Bdnasf/1'>DNA double helix</scene> the <scene name='DNA/Angled_gylcosidic/5'>beta-glycosyl bonds</scene> of bases which are paired <scene name='DNA/Angled_gylcosidic/7'>do not lie opposite</scene> to each other but are positioned at an angle.  
<scene name='DNA/Major_groove/2'>major groove</scene> and the <scene name='DNA/Major_groove/4'>minor groove</scene> of different width and depth. The <scene name='DNA/Major_groove/6'>oxygen atoms of the furanose rings</scene> are on the surface of the minor groove, and the major groove is on the opposite side. The floor or surface of major groove is filled with the <scene name='DNA/Major_floor/2'>atoms of the bases</scene>. The larger size of major groove allows for the binding of DNA specific  proteins.<ref name="Saenger"> Saenger, Wolfram (1984). ''Principles of Nucleic Acid Structure '' (1st ed). Springer-Verlag. pp. 398. ISBN 0-12-645750-6.</ref><ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref>
 
 


[[Image:DNA grooves.png|200px]]


This results in unequally spaced sugar-phosphate backbones and gives rise to <scene name='10/100853/Grooves/2'>two grooves</scene>: the
<scene name='DNA/Major_groove/2'>major groove</scene> and the <scene name='DNA/Major_groove/7'>minor groove</scene> of different width and depth. The <scene name='DNA/Major_groove/8'>oxygen atoms of the furanose rings</scene> are on the surface of the minor groove, and the major groove is on the opposite side. The floor or surface of major groove is filled with the <scene name='DNA/Major_floor/2'>atoms of the bases</scene>. The larger size of major groove allows for the binding of DNA specific  proteins.<ref name="Saenger"> Saenger, Wolfram (1984). ''Principles of Nucleic Acid Structure '' (1st ed). Springer-Verlag. pp. 398. ISBN 0-12-645750-6.</ref><ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref>


== Biological Functions ==  
== Biological Functions ==  
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==Forms of DNA==
==Forms of DNA==
For a comparison of the different forms of DNA, see [[forms of DNA]].
For a comparison of the different forms of DNA, see [[forms of DNA]].
== History of DNA Structure ==
The following summary is copied from an [http://atlas.molviz.org Atlas of Macromolecules] with permission:
:Genes were shown to reside in DNA in 1944 (Avery et al.) and this became widely accepted after the 1952 experiments of Hershey and Chase. The double helical structure of the DNA was predicted by James Watson and Francis Crick in 1953 (Nobel Prize, 1962). Their prediction was based in part upon X-ray diffraction studies by Rosalind Franklin, to whom Watson and Maurice Wilkins gave inadequate credit<ref>Maddox, Brenda: ''Rosalind Franklin: Dark Lady of DNA'', HarperCollins, 2002</ref>. The predicted B-form double helix was not confirmed with atomic-resolution crystal structures until 1973, first by using dinucleotides of RNA (Rosenberg et al.). The first crystal structure containing more than a full turn of the double helix was not solved until 1980 ([[1bna]], 1981, 12 base pairs). The lag of more than a quarter century between prediction and empirical confirmation involved development of [[X-ray crystallography]] for macromolecules, and the need to produce a short, defined sequence of DNA for crystallization. This brief account is based upon a review by Berman, Gelbin, and Westbrook <ref>PMID: 9284453</ref>, where the references will be found.
== DNA Models ==
The model of DNA used in the scenes in the present article is a theoretical model<ref>PMID: 8832384</ref> ([[Image:B-DNA.pdb]]), not available in the [[Protein Data Bank]]. The [[PDB file]] does not follow certain PDB format conventions:
* Bases are designated ADE, CYT, GUA, and THY instead of the standard DA, DC, DG and DT.
* The chains are not named. Typically they would be named A and B.
One chain contains residues numbered 1-12 in sequence CGCG AATT CGCG. The other chain contains residues numbered 13-24 with an identical (antiparallel) sequence.
Theoretical models typically represent idealized DNA conformation, whereas real DNA may have various irregularities including kinks and bends (see examples bound to the [[Lac repressor]]). There are plenty of empirical models for DNA, the first having become available in the 1970's and 80's (see [[#History of DNA Structure|above]]). In May, 2012, the [[Protein Data Bank]] contains nearly 4,000 entries containing DNA. Over 1,300 contain only DNA, while over 2,000 contain protein-DNA complexes. Over 100 entries contain protein, DNA and [[RNA]], and over 100 contain DNA/RNA hybrid molecules.
For more interactive visualizations of DNA, see [http://dna.molviz.org DNA.MolviZ.Org], a tutorial that is available in [http://biomodel.uah.es/model4/dna/ nine languages].
</StructureSection>
</StructureSection>


 
__NOTOC__
== See Also ==
== See Also ==
===Proteopedia Articles===
*[[Forms of DNA]]
*[[Forms of DNA]]
* Kinks vs. Bends in DNA are discussed in [[Lac repressor]].
* [[User:Karsten Theis/DNA bulges|DNA bulges]] occur when a nucleotide is inserted in one strand but not the other, causing an interruption in base pairing.
*[[1ply]]
*[[1ply]]
*[[DNA Replication, Repair, and Recombination]] - Articles in Proteopedia concerning DNA Replication, Repair, and/or Recombination
*[[DNA Replication, Repair, and Recombination]] - Articles in Proteopedia concerning DNA Replication, Repair, and/or Recombination
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*[[tRNA|Transfer ribonucleic acid (tRNA)]]
*[[tRNA|Transfer ribonucleic acid (tRNA)]]
* For additional information, see: [[Nucleic Acids]]
* For additional information, see: [[Nucleic Acids]]
===External Resources===
* [http://dna.molviz.org DNA.MolviZ.Org], an interactive DNA Structure tutorial that is available in [http://biomodel.uah.es/model4/dna/ nine languages].
* [http://bioinformatics.org/molvis/atlas/atlas.htm#dnarna DNA / RNA Section of the Atlas of Macromolecules].
====Interpretation of X-Ray Diffraction by DNA====
* [http://www-tc.pbs.org/wgbh/nova/photo51/media/anatomy.swf Anatomy of Photo 51], Rosalind Franklin's diffraction pattern used by Watson & Crick in developing their model of the DNA double helix (at PBS.Org, US Public Broadcasting System).
* [http://www.dnalc.org/view/15014-Franklin-s-X-ray-diffraction-explanation-of-X-ray-pattern-.html Explanation of Franklin's X-Ray Diffraction Pattern] at Cold Spring Harbor Laboratory, USA.
* More technical: [http://homepages.ius.edu/kforinas/P105/PTE000140.pdf How Rosalind Franklin Discovered the Helical Structure of DNA: Experiments in Diffraction].


== References==
== References==
<references/>
<references/>
[[Category:Featured in BAMBED]]
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