Forms of DNA: Difference between revisions

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''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>


=== A comparative representation of the three forms of DNA ===
<center><b><big><span style="color:red">
''Sources''<ref>http://203.129.231.23/indira/nacc/</ref>
{|
|<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'/>
|<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'/>
|<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'/>
|}
 
{{Clear}}
<center>
'''Synchronize the three applets showing A-, B- and Z-DNA by clicking the checkbox'''
<jmol>
<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <target>A</target>
     <target>A</target>
     <!--<scriptWhenChecked>set syncMouse ON;set syncScript OFF;sync jmolAppletB,jmolAppletZ; sync > "set syncMouse
     <scriptWhenChecked>script applet * @{"set syncMouse on; sync on;"};</scriptWhenChecked>
ON;set syncScript OFF"</scriptWhenChecked>-->
     <scriptWhenUnchecked>script applet * @{"sync off;"};</scriptWhenUnchecked>
            <scriptWhenChecked> sync jmolAppletB,jmolAppletZ </scriptWhenChecked>
     <text>Synchronize rotation of the three models</text>
     <scriptWhenUnchecked> sync OFF</scriptWhenUnchecked>
     <text> Synchronize</text>
</jmolCheckbox>
</jmolCheckbox>
</jmol>
</jmol>
</center>
</span></big></b></center>
<center>To re-align the three molecules, reload this page.</center>
 
{|
|-
!A-DNA
!B-DNA
!Z-DNA
|-
|<applet load='A-DNA.pdb' name='A' size='300' frame='true' scene='User:Adithya_Sagar/Sandbox_DNA/A-dna/1'/>
|<applet load='B-DNA.pdb' name='B' size='300' frame='true' scene='User:Adithya_Sagar/Sandbox_DNA/B-dna/3'/>
|<applet load='Z-DNA.pdb' name='Z' size='300' frame='true' scene='User:Adithya_Sagar/Sandbox_DNA/Z-dna/1'/>
|}


{{Clear}}
{{Clear}}


=== Helical Parameters of the three forms of DNA ===
Change rendering:
<jmol>
  <jmolButton>
    <target>AtoB</target> <!--this is on purpose to the other applet, otherwise "script applet" skips the current one -->
    <script>script applet "A,B,Z" @{"define temp selected; set cartoonRibose on; select all;cartoon -0.01;color cartoon indianRed;select polymer=2;color cartoon darkOrchid;select _P;cpk 35%;select temp;"};</script>
    <text>cartoons</text>
  </jmolButton>
  <jmolButton>
    <target>AtoB</target>
    <script>script applet "A,B,Z" @{"define temp selected;select all;spacefill only;select temp;"};</script>
    <text>spacefilling for all</text>
  </jmolButton>
  <jmolButton>
    <target>AtoB</target>
    <script>script applet "A,B,Z" @{"define temp selected;select all;wireframe -0.3;select temp;"};</script>
    <text>sticks (initial display)</text>
  </jmolButton>
</jmol>
 
== 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>
|}
|}


Line 63: Line 83:


<!-- Generation of smooth transition between animated morphs each of which depicts a different change-->
<!-- Generation of smooth transition between animated morphs each of which depicts a different change-->
<!-- Loading and animating Initial Morph--> 
<jmol>
  <jmolApplet>
    <name>AtoB</name>
    <size>660</size>
    <color>white</color>
    <uploadedFileContents>morph_a-b.pdb</uploadedFileContents>
    <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-->
</jmolApplet>
</jmol>


<!--To activate the below options saving initial state again as restore state after above step is not working-->
<!-- Loading and animating Initial Morph-->  
<jmol>
 
<jmolButton>
<StructureSection load='' name='AtoB' size='550' side='left' caption='Transition between A and B forms of DNA double helix' scene='43/438459/Spacefill_animated/3'>
<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 -->
This animated model displays the structural transformation between A and B forms of 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 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>
<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;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>
    <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;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>
    <text>Transition between A-B DNA spacefilling models</text>
  </item>
  </jmolRadioGroup>
</jmol>


<!-- Restores Original State for Applet 4-->
Rendering: <jmol>
<jmol>
  <jmolButton>
<jmolButton>
    <target>AtoB</target>
<target>AtoB</target>
    <script>wireframe -0.2;</script>
<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>Sticks</text>
<text>Restore Original State </text>
  </jmolButton>
</jmolButton>
  <jmolButton>
</jmol>
    <target>AtoB</target>
    <script>spacefill only; save state ab;</script>
    <text>Spacefill</text>
  </jmolButton>
</jmol> <scene name='43/438459/Spacefill_animated/3'>Reset the model</scene>




<!-- Applet 5-->
Control of animation:<jmol>
<!--<jmol>
<jmolRadioGroup>
   <jmolApplet>
  <target>AtoB</target>
    <color>white</color>
  <vertical>true</vertical>
      <size>660</size>
   <item>
    <uploadedFileContents>Morph_test.pdb</uploadedFileContents>
  <script>frame pause; frame last;</script>
    <script>animation ON;animation mode PALINDROME;cartoon ON; save state ab_new</script>
  <text>A-DNA (without conformational animation)</text>
   </jmolApplet>
  </item>
  <item>
  <script>frame pause; frame rewind;</script>
  <text>B-DNA (without conformational animation)</text>
  </item>
  <item>
  <script>frame play;</script>
   <text>restore animated conformational change</text>
  <checked>true</checked>
  </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>Click here and activate options below </text>
</jmolButton>
</jmol>


<jmol>
<!--Group of actions which show base pair shift, sugar pucker change and difference in space filling models in A and B DNA -->
  <jmolRadioGroup>
Other interesting views:<jmol>
<target>6</target>
<jmolRadioGroup>
<item>
  <target>AtoB</target>
    <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>
  <vertical>true</vertical>
<text>Shift in Base Pair between A-B DNA</text>
  <item>
</item>
  <script>spin off; select all; cartoon only; spacefill 90; wireframe 50; centre all; zoom 180;
color translucent 0.9; select 9:A,4:B; hbonds calculate; hbonds 0.09; color opaque;  
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>
  <text>Shift in base pair between A- and 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!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>
   <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;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>
   <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]]




Line 180: Line 180:
</jmol>-->
</jmol>-->


== References==
</StructureSection>
 
== See also ==
* [[DNA - History of the discovery and current applications (Hebrew)]]
* [[DNA]]
* [[Z-DNA]]
 
== References ==
<references/>
<references/>

Latest revision as of 09:47, 6 July 2025

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 Read more about morphing 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
dA,dT,dC
dG
anti
anti
anti
anti
anti
syn
Sugar pucker
dA,dT,dC
dG
C3'-endo
C3'-endo
C2'-endo
C2'-endo
C2'-endo
C3'-endo
Intrastrand phosphate-phosphate distance [Å]
dA,dT,dC
dG
5.9
5.9
7.0
7.0
7.0
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

See also

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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