B-DNA tour - Revision history

James Nolan at 21:36, 25 January 2021

James Nolan — Mon, 25 Jan 2021 21:36:28 GMT

←Older revision		Revision as of 21:36, 25 January 2021
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	Now change the display to make it show the <scene name='72/725442/Space_filling_bbone/2'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. Notice how they are stacked upon each other and are nearly perpendicular to the axis of the double helix. Note also that the backbone forms a smooth, continuous curve.		Now change the display to make it show the <scene name='72/725442/Space_filling_bbone/2'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. Notice how they are stacked upon each other and are nearly perpendicular to the axis of the double helix. Note also that the backbone forms a smooth, continuous curve.

-	You can <scene name='72/725442/Zoom_pairs/1'>look at just four of the base pairs.</scene>.You are looking into the major groove and the colors of the base pairs alternate. You can also <scene name='72/725442/Zoom_pairs_only/1'>~~looks~~ at just the bases</scene>.	+	You can <scene name='72/725442/Zoom_pairs/1'>look at just four of the base pairs.</scene>.You are looking into the major groove and the colors of the base pairs alternate. You can also <scene name='72/725442/Zoom_pairs_only/1'>look at just the bases</scene>.
	Each base pair stacks on the next similarly, as shown from <scene name='72/725442/Zoom_pairs_top/1'>this top view</scene>. This is the <scene name='72/725442/Zoom_pairs_only_top/1'>same top view of just the bases</scene>. A-form DNA also stacks in this way, but compare this with Z-DNA, which behaves much differently.		Each base pair stacks on the next similarly, as shown from <scene name='72/725442/Zoom_pairs_top/1'>this top view</scene>. This is the <scene name='72/725442/Zoom_pairs_only_top/1'>same top view of just the bases</scene>. A-form DNA also stacks in this way, but compare this with Z-DNA, which behaves much differently.

James Nolan at 13:52, 22 February 2016

James Nolan — Mon, 22 Feb 2016 13:52:11 GMT

←Older revision		Revision as of 13:52, 22 February 2016
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	==B-form DNA==		==B-form DNA==
-	<StructureSection load='1bna' size='400' side='right' caption='B-DNA' scene='72/725442/B-dna_overview/2'>	+	<StructureSection load='1bna' size='400' side='right' caption='B-DNA [[1bna]]' scene='72/725442/B-dna_overview/2'>
	Source <ref>PMID:7071593</ref>		Source <ref>PMID:7071593</ref>
	== Structural highlights ==		== Structural highlights ==

James Nolan at 13:42, 22 February 2016

James Nolan — Mon, 22 Feb 2016 13:42:42 GMT

←Older revision		Revision as of 13:42, 22 February 2016
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	==B-form DNA==		==B-form DNA==
	<StructureSection load='1bna' size='400' side='right' caption='B-DNA' scene='72/725442/B-dna_overview/2'>		<StructureSection load='1bna' size='400' side='right' caption='B-DNA' scene='72/725442/B-dna_overview/2'>
		+	Source <ref>PMID:7071593</ref>
	== Structural highlights ==		== Structural highlights ==
	<UL>		<UL>
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	DNA is usually found in the B form under physiological conditions. The B-form conformation is stabilized by water molecules bound to the minor groove. You can see them as red dots <scene name='72/725442/Water_spine/1'>in this view</scene>. Sometimes kinks are found in the B helix at transcriptional control regions. These kinks can either be intrinsic to the DNA sequence or caused by transcription factor binding.		DNA is usually found in the B form under physiological conditions. The B-form conformation is stabilized by water molecules bound to the minor groove. You can see them as red dots <scene name='72/725442/Water_spine/1'>in this view</scene>. Sometimes kinks are found in the B helix at transcriptional control regions. These kinks can either be intrinsic to the DNA sequence or caused by transcription factor binding.

-	You can compare it with the DNA forms by looking at this [http://proteopedia.org/wiki/images/d/d3/JnABZ3d.gif 3D red-blue ~~stern~~ picture of A, B, and Z DNA]	+	You can compare it with the DNA forms by looking at this [http://proteopedia.org/wiki/images/d/d3/JnABZ3d.gif 3D red-blue stereo picture of A, B, and Z DNA]
	</StructureSection>		</StructureSection>
	==See Also==		==See Also==
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	* An interactive tutorial on [http://dna.molviz.org DNA Structure], ''disponible también en español'' and eight other languages.		* An interactive tutorial on [http://dna.molviz.org DNA Structure], ''disponible también en español'' and eight other languages.
	== References ==		== References ==
-	~~R. E. Dickerson, H. R. Drew, B. N. Conner, R. M. Wing, A. V. Fratini & M.~~	+
-	~~L. Kopka (1982) The anatomy of A-, B-, and Z-DNA. Science 216: 475-485 <ref>PMID:7071593</ref>~~	+
	JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.		JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.


	<references />		<references />

Eric Martz at 00:46, 22 February 2016

Eric Martz — Mon, 22 Feb 2016 00:46:07 GMT

←Older revision		Revision as of 00:46, 22 February 2016
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	* [[A-RNA tour]]		* [[A-RNA tour]]
	* A more general overview will be found at [[DNA]].		* A more general overview will be found at [[DNA]].
-	* [[Forms of DNA]]	+	* [[Forms of DNA]] shows a side-by-side comparison of A, B, and Z forms of DNA.
	* An interactive tutorial on [http://dna.molviz.org DNA Structure], ''disponible también en español'' and eight other languages.		* An interactive tutorial on [http://dna.molviz.org DNA Structure], ''disponible también en español'' and eight other languages.
	== References ==		== References ==

Eric Martz at 00:45, 22 February 2016

Eric Martz — Mon, 22 Feb 2016 00:45:08 GMT

←Older revision		Revision as of 00:45, 22 February 2016
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	</StructureSection>		</StructureSection>
	==See Also==		==See Also==
-	* [[Z DNA model tour]] and [[Z DNA]]	+	* [[Z-DNA model tour]] and [[Z-DNA]]
-	* [[A RNA tour]]	+	* [[A-RNA tour]]
	* A more general overview will be found at [[DNA]].		* A more general overview will be found at [[DNA]].
	* [[Forms of DNA]]		* [[Forms of DNA]]

Eric Martz at 00:43, 22 February 2016

Eric Martz — Mon, 22 Feb 2016 00:43:54 GMT

←Older revision		Revision as of 00:43, 22 February 2016
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	</StructureSection>		</StructureSection>
	==See Also==		==See Also==
-	* [[xx]]	+	* [[Z DNA model tour]] and [[Z DNA]]
		+	* [[A RNA tour]]
		+	* A more general overview will be found at [[DNA]].
		+	* [[Forms of DNA]]
		+	* An interactive tutorial on [http://dna.molviz.org DNA Structure], ''disponible también en español'' and eight other languages.
	== References ==		== References ==
	R. E. Dickerson, H. R. Drew, B. N. Conner, R. M. Wing, A. V. Fratini & M.		R. E. Dickerson, H. R. Drew, B. N. Conner, R. M. Wing, A. V. Fratini & M.

Eric Martz at 00:38, 22 February 2016

Eric Martz — Mon, 22 Feb 2016 00:38:03 GMT

←Older revision		Revision as of 00:38, 22 February 2016
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	You can compare it with the DNA forms by looking at this [http://proteopedia.org/wiki/images/d/d3/JnABZ3d.gif 3D red-blue stern picture of A, B, and Z DNA]		You can compare it with the DNA forms by looking at this [http://proteopedia.org/wiki/images/d/d3/JnABZ3d.gif 3D red-blue stern picture of A, B, and Z DNA]
	</StructureSection>		</StructureSection>
		+	==See Also==
		+	* [[xx]]
	== References ==		== References ==
	R. E. Dickerson, H. R. Drew, B. N. Conner, R. M. Wing, A. V. Fratini & M.		R. E. Dickerson, H. R. Drew, B. N. Conner, R. M. Wing, A. V. Fratini & M.

Eric Martz at 00:31, 22 February 2016

Eric Martz — Mon, 22 Feb 2016 00:31:49 GMT

←Older revision		Revision as of 00:31, 22 February 2016
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	L. Kopka (1982) The anatomy of A-, B-, and Z-DNA. Science 216: 475-485 <ref>PMID:7071593</ref>		L. Kopka (1982) The anatomy of A-, B-, and Z-DNA. Science 216: 475-485 <ref>PMID:7071593</ref>
	JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.		JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
		+
		+
		+	<references />

James Nolan at 14:01, 21 February 2016

James Nolan — Sun, 21 Feb 2016 14:01:38 GMT

←Older revision		Revision as of 14:01, 21 February 2016
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	== Structural highlights ==		== Structural highlights ==
	<UL>		<UL>
-	<LI> Most common DNA conformation in vivo	+	<LI> Most common DNA conformation ''in vivo''
-	<LI> Narrower, more elongated helix than A.	+	<LI> Narrower, more elongated helix than A-form
	<LI> Wide major groove easily accessible to proteins		<LI> Wide major groove easily accessible to proteins
	<LI> Narrow minor groove		<LI> Narrow minor groove
	<LI> Favored conformation at high water concentrations (hydration of minor groove seems to favor B-form)		<LI> Favored conformation at high water concentrations (hydration of minor groove seems to favor B-form)
	<LI> Base pairs nearly perpendicular to helix axis		<LI> Base pairs nearly perpendicular to helix axis
-	<LI> Sugar pucker C2'-endo	+	<LI> Sugar pucker C2'-''endo''
	</UL>		</UL>

James Nolan at 13:58, 21 February 2016

James Nolan — Sun, 21 Feb 2016 13:58:37 GMT

←Older revision		Revision as of 13:58, 21 February 2016
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	==B-form DNA==		==B-form DNA==
-	<StructureSection load='1bna' size='~~340~~' side='right' caption='B-DNA' scene='72/725442/B-dna_overview/~~1''~~'>	+	<StructureSection load='1bna' size='400' side='right' caption='B-DNA' scene='72/725442/B-dna_overview/2'>
	== Structural highlights ==		== Structural highlights ==
	<UL>		<UL>
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	== Take the Tour ==		== Take the Tour ==

-	~~Start the~~ tour with ~~this~~ <scene name='72/725442/B-dna_overview/1'>~~Overview~~</scene> view. Now look at this <scene name='72/725442/Space_filling_view/1'>space filling view</scene>.The backbone is yellow and the bases are magenta. Note that the major groove (in the middle, when you have just clicked the button) is wide and easily accessible.	+	The tour starts with the <scene name='72/725442/B-dna_overview/2'>Default</scene> view. Now look at this <scene name='72/725442/Space_filling_view/2'>space filling view</scene>.The backbone is yellow and the bases are magenta. Note that the major groove (in the middle, when you have just clicked the button) is wide and easily accessible.

-	Now change the display to make it show the <scene name='72/725442/Space_filling_bbone/1'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. Notice how they are stacked upon each other and are nearly perpendicular to the axis of the double helix. Note also that the backbone forms a smooth, continuous curve.	+	Now change the display to make it show the <scene name='72/725442/Space_filling_bbone/2'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. Notice how they are stacked upon each other and are nearly perpendicular to the axis of the double helix. Note also that the backbone forms a smooth, continuous curve.

	You can <scene name='72/725442/Zoom_pairs/1'>look at just four of the base pairs.</scene>.You are looking into the major groove and the colors of the base pairs alternate. You can also <scene name='72/725442/Zoom_pairs_only/1'>looks at just the bases</scene>.		You can <scene name='72/725442/Zoom_pairs/1'>look at just four of the base pairs.</scene>.You are looking into the major groove and the colors of the base pairs alternate. You can also <scene name='72/725442/Zoom_pairs_only/1'>looks at just the bases</scene>.