Forms of DNA: Difference between revisions

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See DNA - History of the discovery and current applications (Hebrew)
== A comparative representation of the three forms of DNA ==
 
''See Also: [[DNA]] and [[Z-DNA]]''
 
=== A comparative representation of the three forms of DNA ===
''Sources'' <ref>Nucleic Acid Canonical Coordinates http://nucleix.mbu.iisc.ac.in/nacc/index.html</ref>
''Sources'' <ref>Nucleic Acid Canonical Coordinates http://nucleix.mbu.iisc.ac.in/nacc/index.html</ref>


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</jmol>
</jmol>


=== Helical Parameters of the three forms of DNA ===
== Helical Parameters of the three forms of DNA ==


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.
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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|Diameter of helix [Å]||align="right"| 23||align="right"| 20||align="right"| 18
|Diameter of helix [Å]||align="right"| 23||align="right"| 20||align="right"| 18
|-
|-
|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
|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
|-
|-
|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
|[[Sugar ring pucker|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
|-
|-
|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
|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
|-
|-
|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>
|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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This animated model displays the structural transformation between A and B forms of DNA.
This animated model displays the structural transformation between A and B forms of DNA.


<jmol>
Rendering: <jmol>
   <jmolButton>
   <jmolButton>
     <target>AtoB</target>
     <target>AtoB</target>
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     <text>Sticks</text>
     <text>Sticks</text>
   </jmolButton>
   </jmolButton>
   <jmolButton>
   <jmolButton>
     <target>AtoB</target>
     <target>AtoB</target>
     <script>spacefill only;</script>
     <script>spacefill only; save state ab;</script>
     <text>Spacefill</text>
     <text>Spacefill</text>
   </jmolButton>
   </jmolButton>
</jmol>
</jmol> <scene name='43/438459/Spacefill_animated/3'>Reset the model</scene>


</StructureSection>


 
Control of animation:<jmol>
<!--To activate the below options saving initial state again as restore state after above step is not working-->
<jmolRadioGroup>
<jmol>
  <target>AtoB</target>
<jmolButton>
  <vertical>true</vertical>
<target>AtoB</target>
   <item>
<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-->
  <script>frame pause; frame last;</script>
<text>Click here and activate the below options </text>
  <text>A-DNA (without conformational animation)</text>
</jmolButton>
  </item>
</jmol>
 
<!--Group of Actions which show base pair shift, sugar pucker change and difference in space filling models in A and B DNA -->
<jmol>
   <jmolRadioGroup>
<target>AtoB</target>
<item>
    <script> moveto 1.0 0 0 1 0 180.0 0.0 0.0;restore state ab; animation mode palindrome;animation ON;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 not 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>
<text>Shift in Base Pair between A-B DNA</text>
</item>
   <item>
   <item>
   <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 not selected; color translucent 0.9; select not 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"; animation mode palindrome;animation ON;</script>
   <script>frame pause; frame rewind;</script>
    <text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
  <text>B-DNA (without conformational animation)</text>
  </item>
  </item>
   <item>
   <item>
   <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 mode PALINDROME;animation ON; set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Transition between A-B DNA spacefilling models"; </script>
   <script>frame play;</script>
    <text>Transition between A-B DNA spacefilling models</text>
  <text>restore animated conformational change</text>
   </item>
   <checked>true</checked>
  </jmolRadioGroup>
  </item>
</jmol>
</jmolRadioGroup>
 
<!-- Restores Original State for Applet 4-->
<jmol>
<jmolButton>
<target>AtoB</target>
<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>
<text>Restore Original State </text>
</jmolButton>
</jmol>
</jmol>




<!-- Applet 5-->
<!--Group of actions which show base pair shift, sugar pucker change and difference in space filling models in A and B DNA -->
<!--<jmol>
Other interesting views:<jmol>
  <jmolApplet>
<jmolRadioGroup>
    <color>white</color>
  <target>AtoB</target>
      <size>660</size>
  <vertical>true</vertical>
    <uploadedFileContents>Morph_test.pdb</uploadedFileContents>
   <item>
    <script>animation ON;animation mode PALINDROME;cartoon ON; save state ab_new</script>
  <script>spin off; select all; cartoon only; spacefill 90; wireframe 50; centre all; zoom 180;
  </jmolApplet>
color translucent 0.9; select 9:A,4:B; hbonds calculate; hbonds 0.09; color opaque;  
</jmol>
set echo bottom centre; font echo 18 serif bold; color echo green; echo "Base pair shift between A and B DNA";
 
moveto 1 0 0 1 0 180 0 0;</script>
<jmol>
  <text>Shift in base pair between A- and B- DNA</text>
<jmolButton>
  </item>
<target>6</target>
<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>
<text>Click here and activate options below </text>
</jmolButton>
</jmol>
 
<jmol>
   <jmolRadioGroup>
<target>6</target>
<item>
    <script> moveto 1.0 0 0 1 0 180.0 0.0 0.0;restore state ab;define temp selected; cartoon ON; spacefill 90; wireframe 50;zoom 180;select 9:a,4:b;hbonds calculate;hbonds 0.09; color translucent 0.9;set echo bottom centre;font echo 20 serif bold;color echo green; echo"Shift in Base Pair between A-B DNA"; select temp; animation mode palindrome;animation ON; </script>
<text>Shift in Base Pair between A-B DNA</text>
</item>
   <item>
   <item>
   <script> moveto 1.0 0 0 1 0 400.0 0.0 0.0; restore state ab;define temp selected; cartoon OFF; spacefill 90; wireframe 50;select not 9:a; color translucent 0.9; centre selected;zoom 400;set echo bottom centre;font echo 20 serif bold;color echo green; echo"Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA"; select temp; refresh; animation mode palindrome;animation ON; </script>
   <script>spin off; select all; spacefill only; spacefill 90; wireframe 50;
    <text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
color translucent 0.9; select 9:A; color opaque; centre selected; zoom 400;  
  </item>
set echo bottom left; font echo 18 serif bold; color echo green; echo "Change in sugar puckering |from C2' endo in B-DNA to C3' endo in A-DNA";
moveto 1 0 0 1 0 400 0 0;</script>
  <text>Change in sugar puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
  </item>
   <item>
   <item>
   <script>moveto 1.0 0 0 1 0 150.0 0.0 0.0;restore state ab;define temp selected; cartoon OFF;spacefill 400; zoom 150; set echo bottom centre;font echo 20 serif bold;color echo green; echo"Transition between A-B DNA spacefilling models"; select temp; animation mode palindrome;animation ON; </script>
   <script>set echo bottom centre; echo;
    <text>Transition between A-B DNA spacefilling models</text>
centre all; moveto 1 {688 565 -455 102.5} 100 0 0; select all; spacefill only; spin on;
  </item>
color opaque;</script>
  </jmolRadioGroup>
  <text>Original display (spacefill)</text>
  </item>
</jmolRadioGroup>
</jmol>
</jmol>


<jmol>
<jmolButton>
<target>6</target>
<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>
<text>Restore Original State </text>
</jmolButton>
</jmol>-->


''Morph Sources'' <ref>PMID: 10734184</ref> / [[Morphs]]
Source of morphs: <ref>PMID: 10734184</ref>  
 
[[Morphs|Read more about morphing]]




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</jmol>-->
</jmol>-->


== References==
</StructureSection>
 
== See also ==
* [[DNA - History of the discovery and current applications (Hebrew)]]
* [[DNA]]
* [[Z-DNA]]
 
== References ==
<references/>
<references/>
Retrieved from "https://proteopedia.org/Forms_of_DNA"