Forms of DNA: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
Angel Herraez (talk | contribs)
Editor, Macro, Print3D, Tester
1,212 edits
rewriting the source code for the aimated transition, to fix nonfunctioning part
Angel Herraez (talk | contribs)
Editor, Macro, Print3D, Tester
1,212 edits
adding extra controls on animation
Line 94: Line 94:
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>
Line 100: Line 100:
     <text>Sticks</text>
     <text>Sticks</text>
   </jmolButton>
   </jmolButton>
   <jmolButton>
   <jmolButton>
     <target>AtoB</target>
     <target>AtoB</target>
Line 106: Line 105:
     <text>Spacefill</text>
     <text>Spacefill</text>
   </jmolButton>
   </jmolButton>
</jmol> <scene name='43/438459/Spacefill_animated/3'>Reset the model</scene>
Control of animation:<jmol>
<jmolRadioGroup>
  <target>AtoB</target>
  <vertical>true</vertical>
  <item>
  <script>frame pause; frame last;</script>
  <text>A-DNA (without conformational animation)</text>
  </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>


<scene name='43/438459/Spacefill_animated/3'>Reset the model</scene>


<!--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:
Other interesting views:<jmol>
<jmol>
  <jmolRadioGroup>
  <jmolRadioGroup>
   <target>AtoB</target>
   <target>AtoB</target>
   <vertical>true</vertical>
   <vertical>true</vertical>
   <item>
   <item>
   <script>moveto 1 0 0 1 0 180 0 0; spin off; select all; cartoon only; spacefill 90; wireframe 50; centre all; zoom 180;  
   <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;  
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";
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>
moveto 1 0 0 1 0 180 0 0;</script>
   <text>Shift in base pair between A- and B- DNA</text>
   <text>Shift in base pair between A- and B- DNA</text>
   </item>
   </item>
   <item>
   <item>
   <script>moveto 1 0 0 1 0 400 0 0; spin off; select all; spacefill only; spacefill 90; wireframe 50;  
   <script>spin off; select all; spacefill only; spacefill 90; wireframe 50;  
color translucent 0.9; select 9:A; color opaque; centre selected; zoom 400;  
color translucent 0.9; select 9:A; color opaque; centre selected; zoom 400;  
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";  
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";
anim mode palindrome; anim on;</script>
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>
   <text>Change in sugar puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
  </item>
  <item>
  <script>set echo bottom centre; echo;
centre all; moveto 1 {688 565 -455 102.5} 100 0 0; select all; spacefill only; spin on;
color opaque;</script>
  <text>Original display (spacefill)</text>
   </item>
   </item>
  </jmolRadioGroup>
  </jmolRadioGroup>
Line 161: Line 185:


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

Revision as of 12:41, 22 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.
Retrieved from "https://proteopedia.org/index.php?title=Forms_of_DNA&oldid=3332803"