Forms of DNA - Revision history

Joel L. Sussman at 09:47, 6 July 2025

2025-07-06T09:47:54Z

← Older revision		Revision as of 09:47, 6 July 2025
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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 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		\|[[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>

Joel L. Sussman at 09:44, 6 July 2025

2025-07-06T09:44:18Z

← Older revision		Revision as of 09:44, 6 July 2025
Line 71:		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\>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 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		\|[[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

Angel Herraez: moving "see also" links to the bottom, and fixing one of them

2023-08-24T17:42:24Z

moving "see also" links to the bottom, and fixing one of them

← Older revision		Revision as of 17:42, 24 August 2023
Line 1:		Line 1:
	~~See DNA - History of the discovery and current applications (Hebrew)~~		== A comparative representation of the three forms of DNA ==

	~~''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>		''Sources'' <ref>Nucleic Acid Canonical Coordinates http://nucleix.mbu.iisc.ac.in/nacc/index.html</ref>

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	</jmol>		</jmol>

	=== Helical Parameters of the three forms of DNA ===		== 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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	</StructureSection>		</StructureSection>

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

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

Karsten Theis at 16:45, 5 January 2022

2022-01-05T16:45:42Z

← Older revision		Revision as of 16:45, 5 January 2022
Line 77:		Line 77:
	\|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\|Sugar ~~ring~~ 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

Karsten Theis at 16:45, 5 January 2022

2022-01-05T16:45:04Z

← Older revision		Revision as of 16:45, 5 January 2022
Line 77:		Line 77:
	\|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 pucker\|Sugar ring 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

Angel Herraez: adding extra controls on animation

2020-12-22T12:41:40Z

adding extra controls on animation

← Older revision		Revision as of 12:41, 22 December 2020
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>
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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>
			</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>
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	</StructureSection>		</StructureSection>

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

Angel Herraez: rewriting the source code for the aimated transition, to fix nonfunctioning part

2020-12-18T19:54:46Z

rewriting the source code for the aimated transition, to fix nonfunctioning part

Show changes

Angel Herraez: new source to fix failures with animated model

2020-12-18T19:05:50Z

new source to fix failures with animated model

← Older revision		Revision as of 19:05, 18 December 2020
Line 90:		Line 90:
	<!-- Loading and animating Initial Morph-->		<!-- Loading and animating Initial Morph-->

	<StructureSection load='' name='AtoB' size='~~600~~' side='left' caption='Transition between A and B forms of DNA double helix' scene='43/438459/Spacefill_animated/3'>		<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'>

	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>		<jmol>
	<jmolButton>		<jmolButton>
Line 99:		Line 100:
	<text>Sticks</text>		<text>Sticks</text>
	</jmolButton>		</jmolButton>

	<jmolButton>		<jmolButton>
	<target>AtoB</target>		<target>AtoB</target>

Angel Herraez at 19:00, 18 December 2020

2020-12-18T19:00:11Z

← Older revision		Revision as of 19:00, 18 December 2020
Line 93:		Line 93:

	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.

	~~<scene name='43/438459/Sticks_animated/1'>Sticks</scene> <scene name='43/438459/Spacefill_animated/3'>Spacefill</scene>~~

	<jmol>		<jmol>
	<jmolButton>		<jmolButton>
Line 101:		Line 98:
	<script>wireframe -0.2;</script>		<script>wireframe -0.2;</script>
	<text>Sticks</text>		<text>Sticks</text>
			</jmolButton>
			<jmolButton>
			<target>AtoB</target>
			<script>spacefill only;</script>
			<text>Spacefill</text>
	</jmolButton>		</jmolButton>
	</jmol>		</jmol>

Angel Herraez at 18:58, 18 December 2020

2020-12-18T18:58:19Z

← Older revision		Revision as of 18:58, 18 December 2020
Line 88:		Line 88:
	<!-- 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-->

	<StructureSection load='' size='~~400~~' side='left' caption='Transition between A and B forms of DNA double helix' scene='43/438459/Spacefill_animated/3'>		<!-- Loading and animating Initial Morph-->

			<StructureSection load='' name='AtoB' size='600' side='left' caption='Transition between A and B forms of DNA double helix' scene='43/438459/Spacefill_animated/3'>

	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.

	<scene name='43/438459/Sticks_animated/1'>Sticks</scene> <scene name='43/438459/Spacefill_animated/3'>Spacefill</scene>		<scene name='43/438459/Sticks_animated/1'>Sticks</scene> <scene name='43/438459/Spacefill_animated/3'>Spacefill</scene>

			<jmol>
			<jmolButton>
			<target>AtoB</target>
			<script>wireframe -0.2;</script>
			<text>Sticks</text>
			</jmolButton>
			</jmol>

	</StructureSection>		</StructureSection>


	~~<!-- 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-->		<!--To activate the below options saving initial state again as restore state after above step is not working-->