Sandbox Z-DNA - Revision history

Adithya Sagar: /* Comparison of the three helices and helical parameters of DNA */

Adithya Sagar — Thu, 23 Jul 2009 06:24:36 GMT

Comparison of the three helices and helical parameters of DNA

←Older revision		Revision as of 06:24, 23 July 2009
Line 70:		Line 70:
	\|Rotation per residue (°) \|\|align="right"\| 33\|\|align="right"\| 36\|\|align="right"\|-30		\|Rotation per residue (°) \|\|align="right"\| 33\|\|align="right"\| 36\|\|align="right"\|-30
	\|-		\|-
-	\|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
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	\|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<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 ~~(A°)~~<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>

Adithya Sagar at 06:18, 23 July 2009

Adithya Sagar — Thu, 23 Jul 2009 06:18:34 GMT

←Older revision		Revision as of 06:18, 23 July 2009
Line 62:		Line 62:
	\|Residues per turn \|\|align="right"\| 11 \|\|align="right"\| 10.5 \|\|align="right"\| 12		\|Residues per turn \|\|align="right"\| 11 \|\|align="right"\| 10.5 \|\|align="right"\| 12
	\|-		\|-
-	\|Axial rise [[Å]] \|\|align="right"\| 2.55 \|\|align="right"\| 3.4 \|\|align="right"\| 3.7	+	\|Axial rise [Å] \|\|align="right"\| 2.55 \|\|align="right"\| 3.4 \|\|align="right"\| 3.7
	\|-		\|-
	\|Helix pitch(°) \|\|align="right"\| 28 \|\|align="right"\| 34 \|\|align="right"\| 45		\|Helix pitch(°) \|\|align="right"\| 28 \|\|align="right"\| 34 \|\|align="right"\| 45
Line 70:		Line 70:
	\|Rotation per residue (°) \|\|align="right"\| 33\|\|align="right"\| 36\|\|align="right"\|-30		\|Rotation per residue (°) \|\|align="right"\| 33\|\|align="right"\| 36\|\|align="right"\|-30
	\|-		\|-
-	\|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

Adithya Sagar at 21:30, 22 July 2009

Adithya Sagar — Wed, 22 Jul 2009 21:30:01 GMT

←Older revision		Revision as of 21:30, 22 July 2009
Line 62:		Line 62:
	\|Residues per turn \|\|align="right"\| 11 \|\|align="right"\| 10.5 \|\|align="right"\| 12		\|Residues per turn \|\|align="right"\| 11 \|\|align="right"\| 10.5 \|\|align="right"\| 12
	\|-		\|-
-	\|Axial rise~~(A°)~~ \|\|align="right"\| 2.55 \|\|align="right"\| 3.4 \|\|align="right"\| 3.7	+	\|Axial rise [[Å]] \|\|align="right"\| 2.55 \|\|align="right"\| 3.4 \|\|align="right"\| 3.7
	\|-		\|-
	\|Helix pitch(°) \|\|align="right"\| 28 \|\|align="right"\| 34 \|\|align="right"\| 45		\|Helix pitch(°) \|\|align="right"\| 28 \|\|align="right"\| 34 \|\|align="right"\| 45
Line 70:		Line 70:
	\|Rotation per residue (°) \|\|align="right"\| 33\|\|align="right"\| 36\|\|align="right"\|-30		\|Rotation per residue (°) \|\|align="right"\| 33\|\|align="right"\| 36\|\|align="right"\|-30
	\|-		\|-
-	\|Diameter of helix ~~(A°)~~ \|\|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

Adithya Sagar: /* Comparison of the three helices and helical parameters of DNA */

Adithya Sagar — Wed, 22 Jul 2009 20:30:29 GMT

Comparison of the three helices and helical parameters of DNA

←Older revision		Revision as of 20:30, 22 July 2009
Line 34:		Line 34:
	== Comparison of the three helices and helical parameters of DNA ==		== Comparison of the three helices and helical parameters of DNA ==
	''Sources''<ref>PMID: 19417072</ref>		''Sources''<ref>PMID: 19417072</ref>
		+
		+	<applet load='A-DNA_ali.pdb' size='350' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>
		+	<applet load='B-DNA_ali.pdb' size='350' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>
		+	<applet load='Z-DNA_ali.pdb' size='350' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>
	<jmol>		<jmol>
	<jmolRadioGroup>		<jmolRadioGroup>
Line 46:		Line 50:
	</jmolRadioGroup>		</jmolRadioGroup>
	</jmol>		</jmol>
-	<applet load='A-DNA_ali.pdb' size='350' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>
-	<applet load='B-DNA_ali.pdb' size='350' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>
-	<applet load='Z-DNA_ali.pdb' size='350' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>
-

	{\| class="wikitable" align= "center''		{\| class="wikitable" align= "center''

Adithya Sagar: /* Comparison of the three helices and helical parameters of DNA */

Adithya Sagar — Wed, 22 Jul 2009 20:29:25 GMT

Comparison of the three helices and helical parameters of DNA

←Older revision		Revision as of 20:29, 22 July 2009
Line 34:		Line 34:
	== Comparison of the three helices and helical parameters of DNA ==		== Comparison of the three helices and helical parameters of DNA ==
	''Sources''<ref>PMID: 19417072</ref>		''Sources''<ref>PMID: 19417072</ref>
-		+	<jmol>
		+	<jmolRadioGroup>
		+	<item>
		+	<script>sync jmolApplet3,jmolApplet4,jmolAppplet5</script>
		+	<text>Synchronize All</text>
		+	</item>
		+	<item>
		+	<script>sync* OFF</script>
		+	<text>Unsynchronize </text>
		+	</item>
		+	</jmolRadioGroup>
		+	</jmol>
	<applet load='A-DNA_ali.pdb' size='350' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>		<applet load='A-DNA_ali.pdb' size='350' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>
	<applet load='B-DNA_ali.pdb' size='350' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>		<applet load='B-DNA_ali.pdb' size='350' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>
	<applet load='Z-DNA_ali.pdb' size='350' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>		<applet load='Z-DNA_ali.pdb' size='350' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>
		+

	{\| class="wikitable" align= "center''		{\| class="wikitable" align= "center''

Adithya Sagar: /* Comparison of the three helices and helical parameters of DNA */

Adithya Sagar — Wed, 22 Jul 2009 20:28:47 GMT

Comparison of the three helices and helical parameters of DNA

←Older revision		Revision as of 20:28, 22 July 2009
Line 35:		Line 35:
	''Sources''<ref>PMID: 19417072</ref>		''Sources''<ref>PMID: 19417072</ref>

-	<applet load='A-DNA_ali.pdb' size='~~351~~' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>	+	<applet load='A-DNA_ali.pdb' size='350' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>
-	<applet load='B-DNA_ali.pdb' size='~~351~~' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>	+	<applet load='B-DNA_ali.pdb' size='350' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>
-	<applet load='Z-DNA_ali.pdb' size='~~351~~' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>	+	<applet load='Z-DNA_ali.pdb' size='350' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>

	{\| class="wikitable" align= "center''		{\| class="wikitable" align= "center''

Adithya Sagar: /* Comparison of the three helices and helical parameters of DNA */

Adithya Sagar — Wed, 22 Jul 2009 20:28:18 GMT

Comparison of the three helices and helical parameters of DNA

←Older revision		Revision as of 20:28, 22 July 2009
Line 35:		Line 35:
	''Sources''<ref>PMID: 19417072</ref>		''Sources''<ref>PMID: 19417072</ref>

-	<applet load='A-DNA_ali.pdb' size='~~348~~' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>	+	<applet load='A-DNA_ali.pdb' size='351' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>
-	<applet load='B-DNA_ali.pdb' size='~~348~~' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>	+	<applet load='B-DNA_ali.pdb' size='351' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>
-	<applet load='Z-DNA_ali.pdb' size='~~348~~' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>	+	<applet load='Z-DNA_ali.pdb' size='351' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>

	{\| class="wikitable" align= "center''		{\| class="wikitable" align= "center''

Adithya Sagar: /* Comparison of the three helices and helical parameters of DNA */

Adithya Sagar — Wed, 22 Jul 2009 20:27:38 GMT

Comparison of the three helices and helical parameters of DNA

←Older revision		Revision as of 20:27, 22 July 2009
Line 35:		Line 35:
	''Sources''<ref>PMID: 19417072</ref>		''Sources''<ref>PMID: 19417072</ref>

-	<applet load='A-DNA_ali.pdb' size='~~345~~' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>	+	<applet load='A-DNA_ali.pdb' size='348' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>
-	<applet load='B-DNA_ali.pdb' size='~~345~~' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>	+	<applet load='B-DNA_ali.pdb' size='348' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>
-	<applet load='Z-DNA_ali.pdb' size='~~345~~' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>	+	<applet load='Z-DNA_ali.pdb' size='348' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>

	{\| class="wikitable" align= "center''		{\| class="wikitable" align= "center''

Adithya Sagar: /* Comparison of the three helices and helical parameters of DNA */

Adithya Sagar — Wed, 22 Jul 2009 20:27:08 GMT

Comparison of the three helices and helical parameters of DNA

←Older revision		Revision as of 20:27, 22 July 2009
Line 35:		Line 35:
	''Sources''<ref>PMID: 19417072</ref>		''Sources''<ref>PMID: 19417072</ref>

-	<applet load='A-DNA_ali.pdb' size='~~340~~' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>	+	<applet load='A-DNA_ali.pdb' size='345' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>
-	<applet load='B-DNA_ali.pdb' size='~~340~~' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>	+	<applet load='B-DNA_ali.pdb' size='345' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>
-	<applet load='Z-DNA_ali.pdb' size='~~340~~' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>	+	<applet load='Z-DNA_ali.pdb' size='345' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>

	{\| class="wikitable" align= "center''		{\| class="wikitable" align= "center''

Adithya Sagar: /* Comparison of the three helices and helical parameters of DNA */

Adithya Sagar — Wed, 22 Jul 2009 20:26:32 GMT

Comparison of the three helices and helical parameters of DNA

←Older revision		Revision as of 20:26, 22 July 2009
Line 35:		Line 35:
	''Sources''<ref>PMID: 19417072</ref>		''Sources''<ref>PMID: 19417072</ref>

-	<applet load='A-DNA_ali.pdb' size='~~360~~' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>	+	<applet load='A-DNA_ali.pdb' size='340' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>
-	<applet load='B-DNA_ali.pdb' size='~~360~~' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>	+	<applet load='B-DNA_ali.pdb' size='340' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>
-	<applet load='Z-DNA_ali.pdb' size='~~360~~' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>	+	<applet load='Z-DNA_ali.pdb' size='340' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>

	{\| class="wikitable" align= "center''		{\| class="wikitable" align= "center''