DNA

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The hydrogen atoms on the bases move from nitrogen or oxygen atom on ring to another through shifts known as tautomeric shifts. However the hydrogens have preferred atomic locations. Based on the movement of hydrogen atoms the nitrogen atoms are in amino or imino configuration and the oxygen atoms are either in keto or enol forms. There is a preference for the amino and keto forms respectively which is very crucial for the biological functioning of DNA as it leads to the specificity 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 hydrogen atoms on the bases move from nitrogen or oxygen atom on ring to another through shifts known as tautomeric shifts. However the hydrogens have preferred atomic locations. Based on the movement of hydrogen atoms the nitrogen atoms are in amino or imino configuration and the oxygen atoms are either in keto or enol forms. There is a preference for the amino and keto forms respectively which is very crucial for the biological functioning of DNA as it leads to the specificity 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>
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</StructureSection>
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== Biological Functions ==
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''Sources:''<ref name='Rawn' > Rawn,David J. "Biochemistry"(1st ed.) Harper&Row,Publishers, Inc.pp. 1024-1050. ISBN-0-06045335-4</ref>
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==Forms of DNA==
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=== Replication===
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''See Also: [[Z-DNA]]''
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DNA undergoes what is known as semi conservative mode of replication wherein the daughter DNA contains one DNA strand of the parent. The replication proceeds through the unwinding of double helix followed by synthesis primers from where the replication begins. An enzyme DNA polymerase synthesizes complementary strands to each parent strand from 5'-3' direction.
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=== A comparative representation of the three forms of DNA ===
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===Transcription and Translation===
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''Sources''<ref>http://203.129.231.23/indira/nacc/</ref>
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The expression of genes into proteins and is a process involving two stages called transcription and translation. In the transcription stage a strand of DNA molecule serves as a template for the synthesis of an RNA molecule called messenger RNA. This messenger RNA is then translated into proteins on ribosomes.
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{|
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|<applet load='A-DNA.pdb' name='A' size='300' frame='true' align='right' caption='A-DNA' align='left' scene='User:Adithya_Sagar/Sandbox_DNA/A-dna/1'/>
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|<applet load='B-DNA.pdb' name='B' size='300' frame='true' align='right' caption='B-DNA' align='left' scene='User:Adithya_Sagar/Sandbox_DNA/B-dna/3'/>
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|<applet load='Z-DNA.pdb' name='Z' size='300' frame='true' align='right' caption='Z-DNA' align='left' scene='User:Adithya_Sagar/Sandbox_DNA/Z-dna/1'/>
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|}
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{{Clear}}
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<center>
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'''Synchronize the three applets showing A-, B- and Z-DNA by clicking the checkbox'''
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<jmol>
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<jmolCheckbox>
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<target>A</target>
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<!--<scriptWhenChecked>set syncMouse ON;set syncScript OFF;sync jmolAppletB,jmolAppletZ; sync > "set syncMouse
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ON;set syncScript OFF"</scriptWhenChecked>-->
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<scriptWhenChecked> sync jmolAppletB,jmolAppletZ </scriptWhenChecked>
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<scriptWhenUnchecked> sync OFF</scriptWhenUnchecked>
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<text> Synchronize</text>
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</center>
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{{Clear}}
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=== Helical Parameters of the three forms of DNA ===
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DNA is a very flexible molecule and has the ability to exist in various forms based on the environmental conditions. Naturally occurring DNA double helices are classified into A, B and Z-types. A and B-forms of DNA are the right handed forms whereas [[Z-DNA]] is the left handed form. When hydrated the DNA generally assumes B-form. The A conformation is found when there is little water to interact with the helix and is also the conformation adopted by the RNA. The formation of Z-DNA occurs with the methylation of deoxycytosine residues and also during transcription where negative supercoiling stabilizes it.
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{| class="wikitable" align= "center''
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|-
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!Parameter
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!A-DNA
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!B-DNA
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!Z-DNA
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|-
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|Helix sense ||align="center"| right-handed ||align="center"| right-handed ||align="center"| left-handed
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|-
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|Residues per turn ||align="right"| 11 ||align="right"| 10.5 ||align="right"| 12
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|-
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|Axial rise [Å] ||align="right"| 2.55 ||align="right"| 3.4 ||align="right"| 3.7
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|-
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|Helix pitch(°) ||align="right"| 28 ||align="right"| 34 ||align="right"| 45
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|-
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|Base pair tilt(°) ||align="right"| 20 ||align="right"| −6 ||align="right"| 7
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|-
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|Rotation per residue (°) ||align="right"| 33||align="right"| 36||align="right"|-30
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|-
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|Diameter of helix [Å]||align="right"| 23||align="right"| 20||align="right"| 18
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|-
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|Glycosidic bond configuration<br\>dA,dT,dC<br\>dG ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>syn
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|-
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|Sugar pucker<br\>dA,dT,dC<br\>dG ||align="center"| <br\>C3'-endo<br\>C3'-endo ||align="center"|<br\> C2'-endo<br\>C2'-endo ||align="center"| <br\>C2'-endo<br\>C3'-endo
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|-
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|Intrastrand phosphate-phosphate distance [Å] <br\>dA,dT,dC<br\>dG ||align="center"| <br\>5.9<br\>5.9||align="center"| <br\>7.0<br\>7.0||align="center"| <br\>7.0<br\> 5.9
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|-
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|colspan="4"|''Sources:<ref name="Rich1984">PMID:6383204</ref><ref name="Rich1979">PMID: 514347</ref><ref> Sinden, Richard R (1994-01-15). ''DNA structure and function'' (1st ed.). Academic Press. pp. 398. ISBN 0-12-645750-6.</ref>
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|}
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== Structural Transformation between A and B DNA ==
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<!-- Generation of smooth transition between animated morphs each of which depicts a different change-->
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<script>animation ON; animation mode PALINDROME; cartoon ON; save state ab </script> <!-- State is saved here when page loads but unable to restore state. It is being required to save state again and then restore works-->
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<!--To activate the below options saving initial state again as restore state after above step is not working-->
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<jmol>
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<target>AtoB</target>
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<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/9/9e/Morph_a-b.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script> <!-- This is required as the initial save state is unable to restore state-->
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<text>Click here and activate the below options </text>
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</jmolButton>
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</jmol>
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<!--Group of Actions which show base pair shift, sugar pucker change and difference in space filling models in A and B DNA -->
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<jmol>
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<target>AtoB</target>
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<item>
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<script> moveto 1.0 0 0 1 0 180.0 0.0 0.0;restore state ab; animation ON;animation mode palindrome;cartoon ON;spacefill on; spacefill 90;wireframe on;wireframe 50;zoom 180;select 9:a,4:b;hbonds ON;hbonds calculate;hbonds 0.09;select!selected; color translucent 0.9;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Base pair shift between A and B DNA"</script>
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<text>Shift in Base Pair between A-B DNA</text>
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</item>
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<item>
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<script> moveto 1.0 0 0 1 0 400.0 0.0 0.0; restore state ab;cartoon OFF;spacefill ON; spacefill 90; wireframe ON; wireframe 50;select 9:a; select!selected; color translucent 0.9; select!selected; centre selected;zoom 400;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA"</script>
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<text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
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</item>
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<item>
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<script>moveto 1.0 0 0 1 0 150.0 0.0 0.0;restore state ab;spacefill ON; spacefill 400; zoom 150; cartoon OFF;animation ON; animation mode PALINDROME;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Transition between A-B DNA spacefilling models"</script>
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<text>Transition between A-B DNA spacefilling models</text>
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<target>AtoB</target>
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<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/9/9e/Morph_a-b.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
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<text>Restore Original State </text>
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</jmolButton>
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<script>animation ON;animation mode PALINDROME;cartoon ON; save state ab_new</script>
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<jmol>
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<target>6</target>
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<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/5/50/Morph_test.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
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<text>Click here and activate options below </text>
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</jmolButton>
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<jmol>
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<script> moveto 1.0 0 0 1 0 180.0 0.0 0.0;restore state ab; animation ON;animation mode palindrome;cartoon ON;spacefill on; spacefill 90;wireframe on;wireframe 50;zoom 180;select 9:a,4:b;hbonds ON;hbonds calculate;hbonds 0.09;select!selected; color translucent 0.9;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Shift in Base Pair between A-B DNA"</script>
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<text>Shift in Base Pair between A-B DNA</text>
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</item>
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<item>
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<script> moveto 1.0 0 0 1 0 400.0 0.0 0.0; restore state ab;cartoon OFF;spacefill ON; spacefill 90; wireframe ON; wireframe 50;select 9:a; select!selected; color translucent 0.9; select!selected; centre selected;zoom 400;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA"</script>
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<text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
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</item>
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<item>
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<script>moveto 1.0 0 0 1 0 150.0 0.0 0.0;restore state ab;spacefill ON; spacefill 400; zoom 150; cartoon OFF;animation ON; animation mode PALINDROME;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Transition between A-B DNA spacefilling models"</script>
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<text>Transition between A-B DNA spacefilling models</text>
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<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/5/50/Morph_test.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
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<text>Restore Original State </text>
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</jmolButton>
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</jmol>-->
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''Morph Sources'' <ref>PMID: 10734184</ref>
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<script>geoSurface ON; geoSurface vdw; color opaque cpk</script>
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<script>spacefill ON; spacefill 600; hide all;color opaque cpk</script>
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<text>Spacefilling Model</text>
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Problems with script synchronization
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<script>geoSurface OFF</script>
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<text>Vanderwaals Surface OFF</text>
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</jmolButton>
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==Forms of DNA==
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For a comparison of the different forms of DNA, see [[forms of DNA]].
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</StructureSection>
== See Also ==
== See Also ==
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*[[Forms of DNA]]
*[[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

Revision as of 22:39, 20 February 2011

B-DNA

Drag the structure with the mouse to rotate


See Also

References

  1. ↑ 1.0 1.1 http://www.genome.gov/25520880
  2. ↑ Dahm R. Discovering DNA: Friedrich Miescher and the early years of nucleic acid research. Hum Genet. 2008 Jan;122(6):565-81. Epub 2007 Sep 28. PMID:17901982 doi:10.1007/s00439-007-0433-0
  3. ↑ 3.0 3.1 3.2 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
  4. ↑ SantaLucia J Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1460-5. PMID:9465037
  5. ↑ Saenger, Wolfram (1984). Principles of Nucleic Acid Structure (1st ed). Springer-Verlag. pp. 398. ISBN 0-12-645750-6.
  6. ↑ Rawn,David J. "Biochemistry"(1st ed.) Harper&Row,Publishers, Inc.pp. 1024-1050. ISBN-0-06045335-4
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