Forms of DNA

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(rewriting the source code for the aimated transition, to fix nonfunctioning part)
(adding extra controls on animation)
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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.
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<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>
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<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>
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</item>
 +
<item>
 +
<script>frame play;</script>
 +
<text>restore animated conformational change</text>
 +
<checked>true</checked>
 +
</item>
 +
</jmolRadioGroup>
</jmol>
</jmol>
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<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 -->
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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";
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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;
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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>
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</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: DNA and Z-DNA

Contents

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
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

References

  1. ↑ Nucleic Acid Canonical Coordinates http://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:http://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.
  5. ↑ Krebs WG, Gerstein M. The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res. 2000 Apr 15;28(8):1665-75. PMID:10734184
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