Z-DNA model tour - Revision history

James Nolan: Undo revision 2705202 by Michal Harel (Talk)

2017-02-20T14:23:08Z

Undo revision 2705202 by Michal Harel (Talk)

←Older revision		Revision as of 14:23, 20 February 2017
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	==Z-form DNA model==		==Z-form DNA model==
	Source <ref>PMID:7071593</ref>		Source <ref>PMID:7071593</ref>
-	<StructureSection load='5zna' size='~~350~~' side='right' caption='Z-DNA [[5zna]]' scene='72/725870/Z-dna_overview/1'>	+	<StructureSection load='5zna' size='400' side='right' caption='Z-DNA [[5zna]]' scene='72/725870/Z-dna_overview/1'>
	== Structural highlights ==		== Structural highlights ==
	<UL>		<UL>

Michal Harel at 21:09, 11 January 2017

2017-01-11T21:09:50Z

←Older revision		Revision as of 21:09, 11 January 2017
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	==Z-form DNA model==		==Z-form DNA model==
	Source <ref>PMID:7071593</ref>		Source <ref>PMID:7071593</ref>
-	<StructureSection load='5zna' size='~~400~~' side='right' caption='Z-DNA [[5zna]]' scene='72/725870/Z-dna_overview/1'>	+	<StructureSection load='5zna' size='350' side='right' caption='Z-DNA [[5zna]]' scene='72/725870/Z-dna_overview/1'>
	== Structural highlights ==		== Structural highlights ==
	<UL>		<UL>

James Nolan at 14:07, 22 February 2016

2016-02-22T14:07:59Z

←Older revision		Revision as of 14:07, 22 February 2016
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	==Z-form DNA model==		==Z-form DNA model==
-	<StructureSection load='5zna' size='400' side='right' caption='B-DNA' scene='72/725870/Z-dna_overview/1'>	+	Source <ref>PMID:7071593</ref>
		+	<StructureSection load='5zna' size='400' side='right' caption='Z-DNA [[5zna]]' scene='72/725870/Z-dna_overview/1'>
	== Structural highlights ==		== Structural highlights ==
	<UL>		<UL>
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	You can compare it with the other 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]		You can compare it with the other 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==
		+	* [[Z-DNA]]
		+	* [[B-DNA tour]]
		+	* [[A-RNA tour]]
		+	* A more general overview will be found at [[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.
	== 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 />

James Nolan at 21:01, 21 February 2016

2016-02-21T21:01:59Z

←Older revision		Revision as of 21:01, 21 February 2016
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	Now change the display to make it show the <scene name='72/725870/Space_filling_bbone/1'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. 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. But notice that the base pairs do not stack upon each other equivalently. The backbone also is not a continuous curve, it "zig-zags" back and forth (hence "Z"-DNA).		Now change the display to make it show the <scene name='72/725870/Space_filling_bbone/1'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. 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. But notice that the base pairs do not stack upon each other equivalently. The backbone also is not a continuous curve, it "zig-zags" back and forth (hence "Z"-DNA).

-	<scene name='72/725870/Zoom_pair/1'>In this view</scene>, the molecule is shown in stick representation, with the backbone in yellow and sets of base pairs in red and blue. Notice how the blue bases stack well on the adjacent blue ones, but not on adjacent red ones, and vice versa. So it is the dinucleotide unit, rather than mononucleotide that is the repeating unit of the structure. This explains the need for alternating purines and pyrimidines to form Z-DNA.	+	<scene name='72/725870/Zoom_pair/2'>In this view</scene>, the molecule is shown in stick representation, with the backbone in yellow and sets of base pairs in red and blue. Notice how the blue bases stack well on the adjacent blue ones, but not on adjacent red ones, and vice versa. So it is the dinucleotide unit, rather than mononucleotide that is the repeating unit of the structure. This explains the need for alternating purines and pyrimidines to form Z-DNA.

-	You can see <scene name='72/725870/Zoom_pairs_only/1'>the same view without the backbone</scene> here.Going 5' to 3', there is good stacking within the GpC dinucleotide, but not between them (CpG).	+	You can see <scene name='72/725870/Zoom_pairs_only/2'>the same view without the backbone</scene> here.Going 5' to 3', there is good stacking within the GpC dinucleotide, but not between them (CpG).
	A <scene name='72/725870/Zoom_pair_top/1'>top view</scene> also illustrates the stacking arrangement. You can also see this <scene name='72/725870/Zoom_pairs_only_top/1'>top view of just the bases.</scene>. Note the stacking of red base pairs on each other is much different than the stacking of red on blue.		A <scene name='72/725870/Zoom_pair_top/1'>top view</scene> also illustrates the stacking arrangement. You can also see this <scene name='72/725870/Zoom_pairs_only_top/1'>top view of just the bases.</scene>. Note the stacking of red base pairs on each other is much different than the stacking of red on blue.

James Nolan at 20:59, 21 February 2016

2016-02-21T20:59:19Z

←Older revision		Revision as of 20:59, 21 February 2016
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	You can see <scene name='72/725870/Zoom_pairs_only/1'>the same view without the backbone</scene> here.Going 5' to 3', there is good stacking within the GpC dinucleotide, but not between them (CpG).		You can see <scene name='72/725870/Zoom_pairs_only/1'>the same view without the backbone</scene> here.Going 5' to 3', there is good stacking within the GpC dinucleotide, but not between them (CpG).
-	A also illustrates the stacking arrangement.	+	A <scene name='72/725870/Zoom_pair_top/1'>top view</scene> also illustrates the stacking arrangement. You can also see this <scene name='72/725870/Zoom_pairs_only_top/1'>top view of just the bases.</scene>. Note the stacking of red base pairs on each other is much different than the stacking of red on blue.
-	. You can also see this	+
-	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]	+	You can compare it with the other 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>
	== References ==		== References ==

James Nolan at 20:46, 21 February 2016

2016-02-21T20:46:01Z

←Older revision		Revision as of 20:46, 21 February 2016
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	Now change the display to make it show the <scene name='72/725870/Space_filling_bbone/1'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. 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. But notice that the base pairs do not stack upon each other equivalently. The backbone also is not a continuous curve, it "zig-zags" back and forth (hence "Z"-DNA).		Now change the display to make it show the <scene name='72/725870/Space_filling_bbone/1'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. 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. But notice that the base pairs do not stack upon each other equivalently. The backbone also is not a continuous curve, it "zig-zags" back and forth (hence "Z"-DNA).

-	~~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>.~~	+	<scene name='72/725870/Zoom_pair/1'>In this view</scene>, the molecule is shown in stick representation, with the backbone in yellow and sets of base pairs in red and blue. Notice how the blue bases stack well on the adjacent blue ones, but not on adjacent red ones, and vice versa. So it is the dinucleotide unit, rather than mononucleotide that is the repeating unit of the structure. This explains the need for alternating purines and pyrimidines to form Z-DNA.
-	~~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~~.	+

-	~~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 see <scene name='72/725870/Zoom_pairs_only/1'>the same view without the backbone</scene> here.Going 5' to 3', there is good stacking within the GpC dinucleotide, but not between them (CpG).
-		+	A also illustrates the stacking arrangement.
-	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 also see this
		+	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>
	== References ==		== References ==

James Nolan at 20:16, 21 February 2016

2016-02-21T20:16:33Z

←Older revision		Revision as of 20:16, 21 February 2016
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	<LI> Narrow minor groove		<LI> Narrow minor groove
	<LI> Conformation favored by high salt concentrations, some base substitutions, but requires alternating purine-pyrimidine sequence.		<LI> Conformation favored by high salt concentrations, some base substitutions, but requires alternating purine-pyrimidine sequence.
-	<!--<LI> N2-amino of G H-bonds to 5' PO: explains slow exchange of proton, need for G purine. -->
	<LI> Base pairs nearly perpendicular to helix axis		<LI> Base pairs nearly perpendicular to helix axis
	<LI> GpC repeat, not single base-pair		<LI> GpC repeat, not single base-pair
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	<LI> Conformations:		<LI> Conformations:
	<UL>		<UL>
-	<LI>G; syn, C2'-endo	+	<LI>G; ''syn'', C2'-''endo''
-	<LI>C; anti, C3'-endo	+	<LI>C; ''anti'', C3'-''endo''
	</UL>		</UL>
	</UL>		</UL>
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	== Take the Tour ==		== Take the Tour ==

-	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~~.	+	The tour starts with the <scene name='72/725870/Z-dna_overview/1'>Default</scene> view. Now look at this <scene name='72/725870/Space_filling_view/1'>space filling view</scene>.The backbone is yellow and the bases are magenta. Note that the major groove (at the top, when you have just clicked the button) is so wide that it is not really a groove any more.

-	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='72/725870/Space_filling_bbone/1'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. 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. But notice that the base pairs do not stack upon each other equivalently. The backbone also is not a continuous curve, it "zig-zags" back and forth (hence "Z"-DNA).

	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>.

James Nolan at 20:03, 21 February 2016

2016-02-21T20:03:03Z

←Older revision		Revision as of 20:03, 21 February 2016
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	==Z-form DNA model==		==Z-form DNA model==
-	<StructureSection load='5zna' size='400' side='right' caption='B-DNA' scene='72/~~725442~~/B-dna_overview/2'>	+	<StructureSection load='5zna' size='400' side='right' caption='B-DNA' scene='72/725870/Z-dna_overview/1'>
	== Structural highlights ==		== Structural highlights ==
	<UL>		<UL>

James Nolan: New page: ==Z-form DNA model== == Structural highlights ==

Helix has left-handed s...

2016-02-21T19:59:34Z

New page: ==Z-form DNA model== <StructureSection load='5zna' size='400' side='right' caption='B-DNA' scene='72/725442/B-dna_overview/2'> == Structural highlights == <UL> <LI> Helix has left-handed s...

New page

==Z-form DNA model==
<StructureSection load='5zna' size='400' side='right' caption='B-DNA' scene='72/725442/B-dna_overview/2'>
== Structural highlights ==
<UL>
<LI> Helix has left-handed sense
<LI> Can be formed in vivo, given proper sequence and superhelical tension, but function remains obscure.
<LI> Narrower, more elongated helix than A or B.
<LI> Major "groove" not really groove
<LI> Narrow minor groove
<LI> Conformation favored by high salt concentrations, some base substitutions, but requires alternating purine-pyrimidine sequence.

<LI> Base pairs nearly perpendicular to helix axis
<LI> GpC repeat, not single base-pair
<UL>
<LI> P-P distances: vary for GpC and CpG
<LI> GpC stack: good base overlap
<LI> CpG: less overlap.
</UL>
<LI> Zigzag backbone due to C sugar conformation compensating for G glycosidic bond conformation
<LI> Conformations:
<UL>
<LI>G; syn, C2'-endo
<LI>C; anti, C3'-endo
</UL>
</UL>

== Take the Tour ==

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/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>.
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.

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]
</StructureSection>
== 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.