1fzx - Revision history

OCA at 18:36, 29 November 2023

OCA — Wed, 29 Nov 2023 18:36:41 GMT

←Older revision		Revision as of 18:36, 29 November 2023
Line 1:		Line 1:

	==NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG==		==NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG==
-	<StructureSection load='1fzx' size='340' side='right'caption='[[1fzx~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>	+	<StructureSection load='1fzx' size='340' side='right'caption='[[1fzx]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FZX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FZX FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'>[[1g14\|1g14]]</div~~></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzx OCA], [https://pdbe.org/1fzx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fzx RCSB], [https://www.ebi.ac.uk/pdbsum/1fzx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fzx ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzx OCA], [https://pdbe.org/1fzx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fzx RCSB], [https://www.ebi.ac.uk/pdbsum/1fzx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fzx ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Herbert, K]]	+	[[Category: Herbert K]]
-	[[Category: Lu, P]]	+	[[Category: Lu P]]
-	[[Category: MacDonald, D]]	+	[[Category: MacDonald D]]
-	[[Category: Pologruto, T]]	+	[[Category: Pologruto T]]
-	[[Category: Zhang, X]]	+	[[Category: Zhang X]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Double helix~~]]	+

OCA at 07:10, 24 March 2021

OCA — Wed, 24 Mar 2021 07:10:19 GMT

←Older revision		Revision as of 07:10, 24 March 2021
Line 3:		Line 3:
	<StructureSection load='1fzx' size='340' side='right'caption='[[1fzx]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1fzx' size='340' side='right'caption='[[1fzx]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1FZX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FZX FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g14\|1g14]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1g14\|1g14]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1fzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzx OCA], [~~http~~://pdbe.org/1fzx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1fzx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1fzx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1fzx ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzx OCA], [https://pdbe.org/1fzx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fzx RCSB], [https://www.ebi.ac.uk/pdbsum/1fzx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fzx ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:05, 19 June 2019

OCA — Wed, 19 Jun 2019 07:05:56 GMT

←Older revision		Revision as of 07:05, 19 June 2019
Line 1:		Line 1:

	==NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG==		==NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG==
-	<StructureSection load='1fzx' size='340' side='right' caption='[[1fzx]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>	+	<StructureSection load='1fzx' size='340' side='right'caption='[[1fzx]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZX FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Herbert, K]]		[[Category: Herbert, K]]
	[[Category: Lu, P]]		[[Category: Lu, P]]

OCA at 10:56, 13 September 2017

OCA — Wed, 13 Sep 2017 10:56:07 GMT

←Older revision		Revision as of 10:56, 13 September 2017
Line 1:		Line 1:
		+
	==NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG==		==NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG==
	<StructureSection load='1fzx' size='340' side='right' caption='[[1fzx]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1fzx' size='340' side='right' caption='[[1fzx]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZX FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g14\|1g14]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g14\|1g14]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzx OCA], [http://pdbe.org/1fzx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fzx RCSB], [http://www.ebi.ac.uk/pdbsum/1fzx PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzx OCA], [http://pdbe.org/1fzx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fzx RCSB], [http://www.ebi.ac.uk/pdbsum/1fzx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1fzx ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:49, 10 September 2015

OCA — Thu, 10 Sep 2015 04:49:49 GMT

←Older revision		Revision as of 04:49, 10 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZX FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g14\|1g14]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g14\|1g14]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fzx RCSB], [http://www.ebi.ac.uk/pdbsum/1fzx PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzx OCA], [http://pdbe.org/1fzx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fzx RCSB], [http://www.ebi.ac.uk/pdbsum/1fzx PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1fzx" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:13, 22 December 2014

OCA — Mon, 22 Dec 2014 06:13:16 GMT

←Older revision		Revision as of 06:13, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZX FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g14\|1g14]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g14\|1g14]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fzx RCSB], [http://www.ebi.ac.uk/pdbsum/1fzx PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fzx RCSB], [http://www.ebi.ac.uk/pdbsum/1fzx PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Herbert, K.]]	+	[[Category: Herbert, K]]
-	[[Category: Lu, P.]]	+	[[Category: Lu, P]]
-	[[Category: MacDonald, D.]]	+	[[Category: MacDonald, D]]
-	[[Category: Pologruto, T.]]	+	[[Category: Pologruto, T]]
-	[[Category: Zhang, X.]]	+	[[Category: Zhang, X]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]

OCA at 05:51, 8 June 2014

OCA — Sun, 08 Jun 2014 05:51:33 GMT

←Older revision		Revision as of 05:51, 8 June 2014
Line 1:		Line 1:
-	[[~~Image:~~1fzx.~~png~~\|~~left~~\|~~200px~~]]	+	==NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG==
		+	<StructureSection load='1fzx' size='340' side='right' caption='[[1fzx]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZX FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g14\|1g14]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fzx RCSB], [http://www.ebi.ac.uk/pdbsum/1fzx PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The solution structure of a DNA dodecamer d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) containing an A-tract has been determined by NMR spectroscopy with residual dipolar couplings. The structure shows an overall helix axis bend of 19 degrees in a geometry consistent with solution and gel electrophoresis experiments. Fourteen degrees of the bending occurs in the GC regions flanking the A-tract. The remaining 5 degrees is spread evenly over its six AT base-pairs. The A-tract is characterized by decreasing minor groove width from the 5' to the 3' direction along the A strand. This is a result of propeller twist in the AT pairs and the increasing negative inclination of the adenine bases at the 3' side of the run of adenine bases. The four central thymine bases all have negative inclination throughout the A-tract with an average value of -6.1 degrees. Although this negative inclination makes the geometry of the A-tract different from all X-ray structures, the proton on N6 of adenine and the O4 of thymine one step down the helix are within distance to form bifurcated hydrogen bonds. The 5' bend of 4 degrees occurs at the junction between the GC flank and the A-tract through a combination of tilt and roll. The larger 3' bend, 10 degrees, occurs in two base steps: the first composed of tilt, -4.1 degrees, and the second a combination of tilt, -4.2 degrees, and roll, 6.0 degrees. This second step is a direct consequence of the change in inclination between an adjacent cytosine base, which has an inclination of -12 degrees, and the next base, a guanine, which has 3 degrees inclination. This bend is a combination of tilt and roll. The large change in inclination allows the formation of a hydrogen bond between the protons of N4 of the 3' cytosine and the O6 of the next 3' base, a guanine, stabilizing the roll component in the bend. These structural features differ from existing models for A-tract bends.For comparison, we also determined the structure of the control sequence, d(GGCAAGAAACGG)/d(CCGTTTCTTGCC), with an AT to GC transition in the center of the A-tract. This structure has no negative inclination in most of the bases within the A-tract, resulting in a bend of only 9 degrees. When ligated in phase, the control sequence has nearly normal mobility in gel electrophoresis experiments.

-	~~{{STRUCTURE_1fzx\| PDB=1fzx \| SCENE= }}~~	+	Solution structure of an A-tract DNA bend.,MacDonald D, Herbert K, Zhang X, Pologruto T, Lu P J Mol Biol. 2001 Mar 9;306(5):1081-98. PMID:11237619<ref>PMID:11237619</ref>

-	~~===NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11237619}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1fzx]] is~~ a ~~2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1FZX OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011237619<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Herbert, K.]]		[[Category: Herbert, K.]]
	[[Category: Lu, P.]]		[[Category: Lu, P.]]

OCA: Protected "1fzx" [edit=sysop:move=sysop]

OCA — Tue, 14 Aug 2012 18:05:16 GMT

Protected "1fzx" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:05, 14 August 2012

OCA at 18:05, 14 August 2012

OCA — Tue, 14 Aug 2012 18:05:14 GMT

←Older revision		Revision as of 18:05, 14 August 2012
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-	{{Seed}}
	[[Image:1fzx.png\|left\|200px]]		[[Image:1fzx.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1fzx", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1fzx\| PDB=1fzx \| SCENE= }}		{{STRUCTURE_1fzx\| PDB=1fzx \| SCENE= }}

	===NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG===		===NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11237619}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11237619 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11237619}}		{{ABSTRACT_PUBMED_11237619}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA].	+	[[1fzx]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA].

	==Reference==		==Reference==
-	~~Solution structure of an A-tract DNA bend., MacDonald D, Herbert K, Zhang X, Pologruto T, Lu P, J Mol Biol. 2001 Mar 9;306(5):1081-98.~~ PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~11237619 11237619]~~	+	<ref group="xtra">PMID:011237619</ref><references group="xtra"/>
	[[Category: Herbert, K.]]		[[Category: Herbert, K.]]
	[[Category: Lu, P.]]		[[Category: Lu, P.]]
Line 29:		Line 17:
	[[Category: Pologruto, T.]]		[[Category: Pologruto, T.]]
	[[Category: Zhang, X.]]		[[Category: Zhang, X.]]
		+	[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 04:11:33 2008''

OCA at 01:11, 1 July 2008

OCA — Tue, 01 Jul 2008 01:11:34 GMT

←Older revision		Revision as of 01:11, 1 July 2008
Line 1:		Line 1:
-	[[Image:1fzx.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1fzx.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1fzx\| PDB=1fzx \| SCENE= }}		{{STRUCTURE_1fzx\| PDB=1fzx \| SCENE= }}

-	~~'''~~NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG~~'''~~	+	===NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG===


-	~~==Overview==~~	+	<!--
-	~~The solution structure of a DNA dodecamer d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) containing an A~~-tract has been determined by NMR spectroscopy with residual dipolar couplings. The structure shows an overall helix axis bend of 19 degrees in a geometry consistent with solution and gel electrophoresis experiments. Fourteen degrees of the bending occurs in the GC regions flanking the A-~~tract.~~ The ~~remaining 5 degrees is spread evenly over its six AT base-pairs. The A-tract is characterized by decreasing minor groove width from~~ the 5' to the 3' direction along the A strand. This is a result of propeller twist in the AT pairs and the increasing negative inclination of the adenine bases at the 3' side of the run of adenine bases. The four central thymine bases all have negative inclination throughout the A-tract with an average value of -6.1 degrees. Although this negative inclination makes the geometry of the A-tract different from all X-ray structures, the proton on ~~N6 of adenine and the O4 of thymine one step down the helix are within distance to form bifurcated hydrogen bonds. The 5' bend of 4 degrees occurs~~ at ~~the junction between the GC flank and the A-tract through a combination of tilt and roll. The larger 3' bend, 10 degrees, occurs in two base steps~~: ~~the first composed of tilt, -4~~.~~1 degrees, and the second a combination of tilt, -4~~.~~2 degrees~~, ~~and roll, 6.0 degrees. This second step~~ is ~~a direct consequence of~~ the ~~change in inclination between an adjacent cytosine base, which has an inclination of -12 degrees, and the next base, a guanine, which has 3 degrees inclination~~. This bend is a combination of tilt and roll. The large change in inclination allows the formation of a hydrogen bond between the protons of N4 of the 3' cytosine and the O6 of the next 3' base, a guanine, stabilizing the roll component in the bend. These structural features differ from existing models for A-~~tract bends.For comparison, we also determined the structure of the control sequence, d(GGCAAGAAACGG)/d(CCGTTTCTTGCC), with an AT to GC transition in the center of the A~~-tract. This structure has no negative inclination in most of the bases within the A-tract, resulting in a bend of only 9 degrees. When ligated in phase, the control sequence has nearly normal mobility in gel electrophoresis experiments.	+	The line below this paragraph, {{ABSTRACT_PUBMED_11237619}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 11237619 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_11237619}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZX OCA].

	==Reference==		==Reference==
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	[[Category: Zhang, X.]]		[[Category: Zhang, X.]]
	[[Category: Double helix]]		[[Category: Double helix]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May~~ ~~2 16~~:57:22 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 04:11:33 2008''