Forms of DNA: Difference between revisions

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Angel Herraez (talk | contribs)
Editor, Macro, Print3D, Tester
1,212 edits
new source to fix failures with animated model
Angel Herraez (talk | contribs)
Editor, Macro, Print3D, Tester
1,212 edits
rewriting the source code for the aimated transition, to fix nonfunctioning part
Line 103: Line 103:
   <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>


</StructureSection>
<scene name='43/438459/Spacefill_animated/3'>Reset the model</scene>
 
 
<!--To activate the below options saving initial state again as restore state after above step is not working-->
<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> <!-- This is required as the initial save state is unable to restore state-->
<text>Click here and activate the below options </text>
</jmolButton>
</jmol>


<!--Group of Actions which show base pair shift, sugar pucker change and difference in space filling models in A and B DNA -->
<!--Group of actions which show base pair shift, sugar pucker change and difference in space filling models in A and B DNA -->
Other interesting views:
<jmol>
<jmol>
  <jmolRadioGroup>
<jmolRadioGroup>
<target>AtoB</target>
  <target>AtoB</target>
<item>
  <vertical>true</vertical>
    <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>moveto 1 0 0 1 0 180 0 0; spin off; select all; cartoon only; spacefill 90; wireframe 50; centre all; zoom 180;  
    <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,4:B; hbonds calculate; hbonds 0.09; color opaque;  
  </item>
set echo bottom centre; font echo 18 serif bold; color echo green; echo "Base pair shift between A and B DNA";
anim mode palindrome; anim on;</script>
  <text>Shift in base pair between A- and B- DNA</text>
  </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>moveto 1 0 0 1 0 400 0 0; spin off; select all; spacefill only; spacefill 90; wireframe 50;
    <text>Transition between A-B DNA spacefilling models</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";
  </jmolRadioGroup>
anim mode palindrome; anim on;</script>
  <text>Change in sugar puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
  </item>
</jmolRadioGroup>
</jmol>
</jmol>


<!-- 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>


Source of morphs: <ref>PMID: 10734184</ref>


<!-- Applet 5-->
[[Morphs|Read more about morphing]]
<!--<jmol>
  <jmolApplet>
    <color>white</color>
      <size>660</size>
    <uploadedFileContents>Morph_test.pdb</uploadedFileContents>
    <script>animation ON;animation mode PALINDROME;cartoon ON; save state ab_new</script>
  </jmolApplet>
</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>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>
  <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>
    <text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
  </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>
    <text>Transition between A-B DNA spacefilling models</text>
  </item>
  </jmolRadioGroup>
</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]]




Line 217: Line 160:
</jmol>-->
</jmol>-->


</StructureSection>
== References==
== References==
<references/>
<references/>

Revision as of 19:54, 18 December 2020

See DNA - History of the discovery and current applications (Hebrew)

See Also: Read more about morphing and Z-DNA

A comparative representation of the three forms of DNA

Sources [1]

To re-align the three molecules, reload this page.
A-DNA B-DNA Z-DNA
Drag the structure with the mouse to rotate
Drag the structure with the mouse to rotate
Drag the structure with the mouse to rotate

Change rendering:

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.

Parameter A-DNA B-DNA Z-DNA
Helix sense right-handed right-handed left-handed
Residues per turn 11 10.5 12
Axial rise [Å] 2.55 3.4 3.7
Helix pitch(°) 28 34 45
Base pair tilt(°) 20 −6 7
Rotation per residue (°) 33 36 -30
Diameter of helix [Å] 23 20 18
Glycosidic bond configuration<br\>dA,dT,dC<br\>dG <br\>anti<br\>anti <br\>anti<br\>anti <br\>anti<br\>syn
Sugar pucker<br\>dA,dT,dC<br\>dG <br\>C3'-endo<br\>C3'-endo <br\> C2'-endo<br\>C2'-endo <br\>C2'-endo<br\>C3'-endo
Intrastrand phosphate-phosphate distance [Å] <br\>dA,dT,dC<br\>dG <br\>5.9<br\>5.9 <br\>7.0<br\>7.0 <br\>7.0<br\> 5.9
Sources: [2][3][4]

Structural Transformation between A and B DNA

Transition between A and B forms of DNA double helix

Drag the structure with the mouse to rotate

References

  1. ↑ Nucleic Acid Canonical Coordinates https://nucleix.mbu.iisc.ac.in/nacc/index.html
  2. ↑ Rich A, Nordheim A, Wang AH. The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem. 1984;53:791-846. PMID:6383204 doi:https://dx.doi.org/10.1146/annurev.bi.53.070184.004043
  3. ↑ Wang AH, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, van der Marel G, Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 1979 Dec 13;282(5740):680-6. PMID:514347
  4. ↑ Sinden, Richard R (1994-01-15). DNA structure and function (1st ed.). Academic Press. pp. 398. ISBN 0-12-645750-6.
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