Forms of DNA: Difference between revisions
From Proteopedia
Jump to navigationJump to search
rewriting the source code for the aimated transition, to fix nonfunctioning part |
No edit summary |
||
| (5 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
== 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> | ||
| Line 50: | Line 46: | ||
</jmol> | </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. | ||
| Line 75: | Line 71: | ||
|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 | |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 | |[[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 | |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 94: | Line 90: | ||
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 96: | ||
<text>Sticks</text> | <text>Sticks</text> | ||
</jmolButton> | </jmolButton> | ||
<jmolButton> | <jmolButton> | ||
<target>AtoB</target> | <target>AtoB</target> | ||
| Line 106: | Line 101: | ||
<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> | ||
<!--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> | <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"; | ||
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> | <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"; | ||
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 181: | ||
</StructureSection> | </StructureSection> | ||
== References== | |||
== See also == | |||
* [[DNA - History of the discovery and current applications (Hebrew)]] | |||
* [[DNA]] | |||
* [[Z-DNA]] | |||
== References == | |||
<references/> | <references/> | ||
