1rvi - Revision history

OCA at 09:22, 6 December 2023

OCA — Wed, 06 Dec 2023 09:22:23 GMT

←Older revision		Revision as of 09:22, 6 December 2023
Line 1:		Line 1:

	==SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG==		==SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG==
-	<StructureSection load='1rvi' size='340' side='right'caption='[[1rvi~~]], [[NMR_Ensembles_of_Models \| 9 NMR models~~]]' scene=''>	+	<StructureSection load='1rvi' size='340' side='right'caption='[[1rvi]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVI 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;'>[[1rvh\|1rvh]]</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=1rvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvi OCA], [https://pdbe.org/1rvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rvi RCSB], [https://www.ebi.ac.uk/pdbsum/1rvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvi 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=1rvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvi OCA], [https://pdbe.org/1rvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rvi RCSB], [https://www.ebi.ac.uk/pdbsum/1rvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvi ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Feigon, J]]	+	[[Category: Feigon J]]
-	[[Category: Ravindranathan, S]]	+	[[Category: Ravindranathan S]]
-	[[Category: Sklenar, V]]	+	[[Category: Sklenar V]]
-	[[Category: Stefl, R]]	+	[[Category: Stefl R]]
-	[[Category: Wu, H]]	+	[[Category: Wu H]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Double helix~~]]	+

OCA at 07:22, 22 September 2021

OCA — Wed, 22 Sep 2021 07:22:48 GMT

←Older revision		Revision as of 07:22, 22 September 2021
Line 3:		Line 3:
	<StructureSection load='1rvi' size='340' side='right'caption='[[1rvi]], [[NMR_Ensembles_of_Models \| 9 NMR models]]' scene=''>		<StructureSection load='1rvi' size='340' side='right'caption='[[1rvi]], [[NMR_Ensembles_of_Models \| 9 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1RVI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVI FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rvh\|1rvh]]</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;'>[[1rvh\|1rvh]]</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=1rvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvi OCA], [~~http~~://pdbe.org/1rvi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1rvi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1rvi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvi 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=1rvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvi OCA], [https://pdbe.org/1rvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rvi RCSB], [https://www.ebi.ac.uk/pdbsum/1rvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvi ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:24, 11 December 2019

OCA — Wed, 11 Dec 2019 19:24:47 GMT

←Older revision		Revision as of 19:24, 11 December 2019
Line 1:		Line 1:

	==SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG==		==SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG==
-	<StructureSection load='1rvi' size='340' side='right' caption='[[1rvi]], [[NMR_Ensembles_of_Models \| 9 NMR models]]' scene=''>	+	<StructureSection load='1rvi' size='340' side='right'caption='[[1rvi]], [[NMR_Ensembles_of_Models \| 9 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVI FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Feigon, J]]		[[Category: Feigon, J]]
	[[Category: Ravindranathan, S]]		[[Category: Ravindranathan, S]]

OCA at 06:56, 8 March 2018

OCA — Thu, 08 Mar 2018 06:56:14 GMT

←Older revision		Revision as of 06:56, 8 March 2018
Line 1:		Line 1:
		+
	==SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG==		==SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG==
	<StructureSection load='1rvi' size='340' side='right' caption='[[1rvi]], [[NMR_Ensembles_of_Models \| 9 NMR models]]' scene=''>		<StructureSection load='1rvi' size='340' side='right' caption='[[1rvi]], [[NMR_Ensembles_of_Models \| 9 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVI FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rvh\|1rvh]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rvh\|1rvh]]</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=1rvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvi OCA], [http://pdbe.org/1rvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rvi RCSB], [http://www.ebi.ac.uk/pdbsum/1rvi 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=1rvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvi OCA], [http://pdbe.org/1rvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rvi RCSB], [http://www.ebi.ac.uk/pdbsum/1rvi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvi ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:54, 10 September 2015

OCA — Thu, 10 Sep 2015 04:54:39 GMT

←Older revision		Revision as of 04:54, 10 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVI FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rvh\|1rvh]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rvh\|1rvh]]</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=1rvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rvi RCSB], [http://www.ebi.ac.uk/pdbsum/1rvi 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=1rvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvi OCA], [http://pdbe.org/1rvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rvi RCSB], [http://www.ebi.ac.uk/pdbsum/1rvi 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 1rvi" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:12, 8 December 2014

OCA — Mon, 08 Dec 2014 09:12:22 GMT

←Older revision		Revision as of 09:12, 8 December 2014
Line 1:		Line 1:
-	[[~~Image:~~1rvi.~~png~~\|~~left~~\|~~200px~~]]	+	==SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG==
		+	<StructureSection load='1rvi' size='340' side='right' caption='[[1rvi]], [[NMR_Ensembles_of_Models \| 9 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVI FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rvh\|1rvh]]</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=1rvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rvi RCSB], [http://www.ebi.ac.uk/pdbsum/1rvi PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA A-tracts have been defined as four or more consecutive A.T base pairs without a TpA step. When inserted in phase with the DNA helical repeat, bending is manifested macroscopically as anomalous migration on polyacrylamide gels, first observed >20 years ago. An unsolved conundrum is why DNA containing in-phase A-tract repeats of A(4)T(4) are bent, whereas T(4)A(4) is straight. We have determined the solution structures of the DNA duplexes formed by d(GCAAAATTTTGC) [A4T4] and d(CGTTTTAAAACG) [T4A4] with NH(4)(+) counterions by using NMR spectroscopy, including refinement with residual dipolar couplings. Analysis of the structures shows that the ApT step has a large negative roll, resulting in a local bend toward the minor groove, whereas the TpA step has a positive roll and locally bends toward the major groove. For A4T4, this bend is nearly in phase with bends at the two A-tract junctions, resulting in an overall bend toward the minor groove of the A-tract, whereas for T4A4, the bends oppose each other, resulting in a relatively straight helix. NMR-based structural modeling of d(CAAAATTTTG)(15) and d(GTTTTAAAAC)(15) reveals that the former forms a left-handed superhelix with a diameter of approximately 110 A and pitch of 80 A, similar to DNA in the nucleosome, whereas the latter has a gentle writhe with a pitch of >250 A and diameter of approximately 50 A. Results of gel electrophoretic mobility studies are consistent with the higher-order structure of the DNA and furthermore depend on the nature of the monovalent cation present in the running buffer.

-	~~{{STRUCTURE_1rvi\| PDB=1rvi \| SCENE= }}~~	+	DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum.,Stefl R, Wu H, Ravindranathan S, Sklenar V, Feigon J Proc Natl Acad Sci U S A. 2004 Feb 3;101(5):1177-82. Epub 2004 Jan 22. PMID:14739342<ref>PMID:14739342</ref>

-	~~===SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_14739342}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1rvi]] is~~ a ~~2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1RVI OCA].~~	+	</StructureSection>
-		+	[[Category: Feigon, J]]
-	==~~Reference~~==	+	[[Category: Ravindranathan, S]]
-	<~~ref group="xtra">PMID:014739342<~~/~~ref~~><~~references group="xtra"~~/>	+	[[Category: Sklenar, V]]
-	[[Category: Feigon, J.]]	+	[[Category: Stefl, R]]
-	[[Category: Ravindranathan, S.]]	+	[[Category: Wu, H]]
-	[[Category: Sklenar, V.]]	+
-	[[Category: Stefl, R.]]	+
-	[[Category: Wu, H.]]	+
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]

OCA at 15:06, 6 March 2013

OCA — Wed, 06 Mar 2013 15:06:24 GMT

←Older revision		Revision as of 15:06, 6 March 2013
Line 1:		Line 1:
	[[Image:1rvi.png\|left\|200px]]		[[Image:1rvi.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1rvi", 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_1rvi\| PDB=1rvi \| SCENE= }}		{{STRUCTURE_1rvi\| PDB=1rvi \| SCENE= }}

	===SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG===		===SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_14739342}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 14739342 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_14739342}}		{{ABSTRACT_PUBMED_14739342}}

	==About this Structure==		==About this Structure==
	[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA].		[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA].
-
-	==See Also==
-	*[[Group:SMART:Greenwood SMART Team]]

	==Reference==		==Reference==

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

OCA — Wed, 04 May 2011 10:14:49 GMT

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

←Older revision

Revision as of 10:14, 4 May 2011

OCA at 10:14, 4 May 2011

OCA — Wed, 04 May 2011 10:14:48 GMT

←Older revision		Revision as of 10:14, 4 May 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1rvi.png\|left\|200px]]		[[Image:1rvi.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA].	+	[[1rvi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVI OCA].
		+
		+	==See Also==
		+	*[[Group:SMART:Greenwood SMART Team]]

	==Reference==		==Reference==
-	DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum., Stefl R, Wu H, Ravindranathan S, Sklenar V, Feigon J, Proc Natl Acad Sci U S A. 2004 Feb 3;101(5):1177-82. Epub 2004 Jan 22. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~14739342 14739342]~~	+	<ref group="xtra">PMID:014739342</ref><references group="xtra"/>
	[[Category: Feigon, J.]]		[[Category: Feigon, J.]]
	[[Category: Ravindranathan, S.]]		[[Category: Ravindranathan, S.]]
Line 29:		Line 31:
	[[Category: Stefl, R.]]		[[Category: Stefl, R.]]
	[[Category: Wu, H.]]		[[Category: Wu, H.]]
		+	[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 19:37:56 2008''

OCA at 16:37, 27 July 2008

OCA — Sun, 27 Jul 2008 16:37:59 GMT

←Older revision		Revision as of 16:37, 27 July 2008
Line 1:		Line 1:
-	[[Image:1rvi.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1rvi.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1rvi\| PDB=1rvi \| SCENE= }}		{{STRUCTURE_1rvi\| PDB=1rvi \| SCENE= }}

-	~~'''~~SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG~~'''~~	+	===SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG===


-	~~==Overview==~~	+	<!--
-	~~DNA A-tracts have been defined as four or more consecutive A.T base pairs without a TpA step. When inserted in phase with the DNA helical repeat~~, ~~bending is manifested macroscopically as anomalous migration on polyacrylamide gels~~, ~~first observed >20 years ago. An unsolved conundrum is why DNA containing in-phase A-tract repeats of A(4)T(4) are bent, whereas T(4)A(4) is straight. We have determined~~ the ~~solution structures of~~ the ~~DNA duplexes formed by d~~(~~GCAAAATTTTGC) [A4T4] and d(CGTTTTAAAACG) [T4A4] with NH(4)(+) counterions by using NMR spectroscopy, including refinement with residual dipolar couplings~~. Analysis of the structures shows that the ApT step has a large negative roll, resulting in a local bend toward the minor groove, whereas the TpA step has a positive roll and locally bends toward the major groove. ~~For A4T4~~, ~~this bend~~ is ~~nearly in phase with bends at~~ the ~~two A-tract junctions, resulting in an overall bend toward the minor groove of the A-tract, whereas for T4A4, the bends oppose each other, resulting in a relatively straight helix~~. ~~NMR~~-~~based structural modeling of d(CAAAATTTTG)(15) and d(GTTTTAAAAC)(15) reveals that the former forms a left~~-handed superhelix with a diameter of approximately 110 A and pitch of 80 A, similar to DNA in the nucleosome, whereas the latter has a gentle writhe with a pitch of >250 A and diameter of approximately 50 A. Results of gel electrophoretic mobility studies are consistent with the higher-order structure of the DNA and furthermore depend on the nature of the monovalent cation present in the running buffer.	+	The line below this paragraph, {{ABSTRACT_PUBMED_14739342}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 14739342 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_14739342}}

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

	==Reference==		==Reference==
Line 26:		Line 30:
	[[Category: Wu, H.]]		[[Category: Wu, H.]]
	[[Category: Double helix]]		[[Category: Double helix]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 07~~:57:34 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 19:37:56 2008''