1buf - Revision history

OCA at 11:37, 22 November 2023

2023-11-22T11:37:41Z

← Older revision		Revision as of 11:37, 22 November 2023
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	==SELF-COMPLEMENTARY DNA 5'-D(CAATTG)2, NMR, MINIMIZED AVERAGE STRUCTURE==		==SELF-COMPLEMENTARY DNA 5'-D(CAATTG)2, NMR, MINIMIZED AVERAGE STRUCTURE==
	<StructureSection load='1buf' size='340' side='right'caption='[[1buf~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>		<StructureSection load='1buf' size='340' side='right'caption='[[1buf]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1buf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BUF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1buf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BUF 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;'>[[1uqa\|1uqa]], [[1uqb\|1uqb]], [[1uqc\|1uqc]], [[1uqd\|1uqd]], [[1uqe\|1uqe]], [[1uqf\|1uqf]], [[1uqg\|1uqg]]</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=1buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1buf OCA], [https://pdbe.org/1buf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1buf RCSB], [https://www.ebi.ac.uk/pdbsum/1buf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1buf 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=1buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1buf OCA], [https://pdbe.org/1buf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1buf RCSB], [https://www.ebi.ac.uk/pdbsum/1buf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1buf ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Au-Yeung~~, S C.F~~]]		[[Category: Au-Yeung SCF]]
	[[Category: Lam~~, S L]]~~		[[Category: Lam SL]]
	~~[[Category: Deoxyribonucleic acid]]~~
	~~[[Category: Dna~~]]

OCA at 07:02, 24 February 2021

2021-02-24T07:02:38Z

← Older revision		Revision as of 07:02, 24 February 2021
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	<StructureSection load='1buf' size='340' side='right'caption='[[1buf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1buf' size='340' side='right'caption='[[1buf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1buf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1BUF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1buf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BUF FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uqa\|1uqa]], [[1uqb\|1uqb]], [[1uqc\|1uqc]], [[1uqd\|1uqd]], [[1uqe\|1uqe]], [[1uqf\|1uqf]], [[1uqg\|1uqg]]</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;'>[[1uqa\|1uqa]], [[1uqb\|1uqb]], [[1uqc\|1uqc]], [[1uqd\|1uqd]], [[1uqe\|1uqe]], [[1uqf\|1uqf]], [[1uqg\|1uqg]]</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=1buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1buf OCA], [~~http~~://pdbe.org/1buf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1buf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1buf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1buf 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=1buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1buf OCA], [https://pdbe.org/1buf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1buf RCSB], [https://www.ebi.ac.uk/pdbsum/1buf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1buf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:20, 21 May 2019

2019-05-21T09:20:00Z

← Older revision		Revision as of 09:20, 21 May 2019
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	==SELF-COMPLEMENTARY DNA 5'-D(CAATTG)2, NMR, MINIMIZED AVERAGE STRUCTURE==		==SELF-COMPLEMENTARY DNA 5'-D(CAATTG)2, NMR, MINIMIZED AVERAGE STRUCTURE==
	<StructureSection load='1buf' size='340' side='right' caption='[[1buf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1buf' size='340' side='right'caption='[[1buf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1buf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1buf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUF FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Au-Yeung, S C.F]]		[[Category: Au-Yeung, S C.F]]
	[[Category: Lam, S L]]		[[Category: Lam, S L]]
	[[Category: Deoxyribonucleic acid]]		[[Category: Deoxyribonucleic acid]]
	[[Category: Dna]]		[[Category: Dna]]

OCA at 06:13, 17 August 2017

2017-08-17T06:13:23Z

← Older revision		Revision as of 06:13, 17 August 2017
Line 1:		Line 1:

	==SELF-COMPLEMENTARY DNA 5'-D(CAATTG)2, NMR, MINIMIZED AVERAGE STRUCTURE==		==SELF-COMPLEMENTARY DNA 5'-D(CAATTG)2, NMR, MINIMIZED AVERAGE STRUCTURE==
	<StructureSection load='1buf' size='340' side='right' caption='[[1buf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1buf' size='340' side='right' caption='[[1buf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
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	<table><tr><td colspan='2'>[[1buf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1buf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUF FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uqa\|1uqa]], [[1uqb\|1uqb]], [[1uqc\|1uqc]], [[1uqd\|1uqd]], [[1uqe\|1uqe]], [[1uqf\|1uqf]], [[1uqg\|1uqg]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uqa\|1uqa]], [[1uqb\|1uqb]], [[1uqc\|1uqc]], [[1uqd\|1uqd]], [[1uqe\|1uqe]], [[1uqf\|1uqf]], [[1uqg\|1uqg]]</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=1buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1buf OCA], [http://pdbe.org/1buf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1buf RCSB], [http://www.ebi.ac.uk/pdbsum/1buf 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=1buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1buf OCA], [http://pdbe.org/1buf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1buf RCSB], [http://www.ebi.ac.uk/pdbsum/1buf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1buf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:18, 9 September 2015

2015-09-09T23:18:33Z

← Older revision		Revision as of 23:18, 9 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1buf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1buf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUF FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uqa\|1uqa]], [[1uqb\|1uqb]], [[1uqc\|1uqc]], [[1uqd\|1uqd]], [[1uqe\|1uqe]], [[1uqf\|1uqf]], [[1uqg\|1uqg]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uqa\|1uqa]], [[1uqb\|1uqb]], [[1uqc\|1uqc]], [[1uqd\|1uqd]], [[1uqe\|1uqe]], [[1uqf\|1uqf]], [[1uqg\|1uqg]]</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=1buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1buf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1buf RCSB], [http://www.ebi.ac.uk/pdbsum/1buf 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=1buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1buf OCA], [http://pdbe.org/1buf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1buf RCSB], [http://www.ebi.ac.uk/pdbsum/1buf PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 1buf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:14, 22 December 2014

2014-12-22T11:14:44Z

← Older revision		Revision as of 11:14, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1buf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1buf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUF FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uqa\|1uqa]], [[1uqb\|1uqb]], [[1uqc\|1uqc]], [[1uqd\|1uqd]], [[1uqe\|1uqe]], [[1uqf\|1uqf]], [[1uqg\|1uqg]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uqa\|1uqa]], [[1uqb\|1uqb]], [[1uqc\|1uqc]], [[1uqd\|1uqd]], [[1uqe\|1uqe]], [[1uqf\|1uqf]], [[1uqg\|1uqg]]</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=1buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1buf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1buf RCSB], [http://www.ebi.ac.uk/pdbsum/1buf 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=1buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1buf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1buf RCSB], [http://www.ebi.ac.uk/pdbsum/1buf PDBsum]</span></td></tr>
	<table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Au-Yeung, S C.F.]]		[[Category: Au-Yeung, S C.F]]
	[[Category: Lam, S L.]]		[[Category: Lam, S L]]
	[[Category: Deoxyribonucleic acid]]		[[Category: Deoxyribonucleic acid]]
	[[Category: Dna]]		[[Category: Dna]]

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

2014-06-08T05:49:32Z

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

← Older revision	Revision as of 05:49, 8 June 2014
(No difference)

OCA at 05:49, 8 June 2014

2014-06-08T05:49:29Z

← Older revision		Revision as of 05:49, 8 June 2014
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	~~{{Seed}}~~		==SELF-COMPLEMENTARY DNA 5'-D(CAATTG)2, NMR, MINIMIZED AVERAGE STRUCTURE==
	[[~~Image~~:~~1buf~~.~~png~~\|~~left~~\|~~200px~~]]		<StructureSection load='1buf' size='340' side='right' caption='[[1buf]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[1buf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUF FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uqa\|1uqa]], [[1uqb\|1uqb]], [[1uqc\|1uqc]], [[1uqd\|1uqd]], [[1uqe\|1uqe]], [[1uqf\|1uqf]], [[1uqg\|1uqg]]</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=1buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1buf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1buf RCSB], [http://www.ebi.ac.uk/pdbsum/1buf PDBsum]</span></td></tr>
			<table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			In this study, the solution structures of eight self-complementary deoxyribonucleic acid molecules, d(CGXX'CG)2 and d(CAXX'TG)2 (where X = C, G, T or A and X' is complementary to X), have been determined using NMR interproton distances, endocyclic sugar torsion angles, backbone torsion angles and hydrogen bond constraints. Based on the structural data obtained in solution, a novel sequence-specific local structure function, sigma LS, composed of the sum of the contributions from the helix twist omega, base roll rho, base-pair slide delta delta and propeller twist omega, is introduced to describe their sequence-specific local structures. Sigma LS is found to produce an acceptable correlation (r = 0.96) with the relative local stability (delta G0 10) of a base-pair-step. This result demonstrates that in addition to the inter-strand purine-purine clashes, the base morphology of nearest-neighbor base-pairs is also important in defining the local geometry of base-pairs. Thus, in analyzing the base-pair structural parameter blocks of trimers are used as the basic unit whereas for the base-pair-step structural parameters, the basic unit is composed of blocks of tetramers. The omega LS-delta G(zero) 10 correlation is the first experimental evidence demonstrating the relationship between the relative local stabilities and the sequence-specific local structures of DNA duplexes. It also forms the basis for using the trimer-tetramer model for the prediction of sequence-specific local structures of deoxyribonucleic acid molecules.

	<!--		Sequence-specific local structural variations in solution structures of d(CGXX'CG)2 and d(CAXX'TG)2 self-complementary deoxyribonucleic acids.,Lam SL, Au-Yeung SC J Mol Biol. 1997 Mar 7;266(4):745-60. PMID:9102467<ref>PMID:9102467</ref>
	~~The line below this paragraph~~, ~~containing "STRUCTURE_1buf"~~, ~~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_1buf\| PDB=1buf \| SCENE= }}~~

	~~===SELF-COMPLEMENTARY DNA 5'-D(CAATTG)2~~, ~~NMR, MINIMIZED AVERAGE STRUCTURE===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			== References ==
	~~<!--~~		<references/>
	~~The line below this paragraph, {{ABSTRACT_PUBMED_9102467}}, adds the Publication Abstract to~~ the ~~page~~		__TOC__
	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 9102467 is the PubMed ID number~~.		</StructureSection>
	-->
	~~{{ABSTRACT_PUBMED_9102467}}~~

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

	~~==Reference==~~
	Sequence-specific local structural variations in solution structures of d(CGXX'CG)2 and d(CAXX'TG)2 self-complementary deoxyribonucleic acids., Lam SL, Au-Yeung SC, J Mol Biol. 1997 Mar 7;266(4):745-60. PMID:[http:/~~/www.ncbi.nlm.nih.gov/pubmed/9102467 9102467]~~
	[[Category: Au-Yeung, S C.F.]]		[[Category: Au-Yeung, S C.F.]]
	[[Category: Lam, S L.]]		[[Category: Lam, S L.]]
	[[Category: Deoxyribonucleic acid]]		[[Category: Deoxyribonucleic acid]]
	[[Category: Dna]]		[[Category: Dna]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 19:44:15 2008''~~

OCA at 16:44, 30 June 2008

2008-06-30T16:44:17Z

← Older revision		Revision as of 16:44, 30 June 2008
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	[[Image:1buf.~~jpg~~\|left\|200px]]		{{Seed}}
			[[Image:1buf.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1buf\| PDB=1buf \| SCENE= }}		{{STRUCTURE_1buf\| PDB=1buf \| SCENE= }}

	~~'''~~SELF-COMPLEMENTARY DNA 5'-D(CAATTG)2, NMR, MINIMIZED AVERAGE STRUCTURE~~'''~~		===SELF-COMPLEMENTARY DNA 5'-D(CAATTG)2, NMR, MINIMIZED AVERAGE STRUCTURE===


	~~==Overview==~~		<!--
	In this study, the solution structures of eight self-complementary deoxyribonucleic acid molecules, d(CGXX'CG)2 and d(CAXX'TG)2 (where X = C, G, T or A and X' is complementary to X), have been determined using NMR interproton distances, endocyclic sugar torsion angles, backbone torsion angles and hydrogen bond constraints. Based on the structural data obtained in solution, a novel sequence-specific local structure function, ~~sigma LS~~, ~~composed of~~ the sum of the contributions from the helix twist omega, base roll rho, base-pair slide delta delta and propeller twist omega, is introduced to describe their sequence-specific local structures. Sigma LS is found to ~~produce an acceptable correlation (r = 0.96) with~~ the ~~relative local stability~~ (~~delta G0 10) of a base-pair-step~~. ~~This result demonstrates that in addition to the inter-strand purine-purine clashes, the base morphology of nearest-neighbor base-pairs is also important in defining the local geometry of base-pairs~~. ~~Thus~~, in analyzing the base-pair structural parameter blocks of trimers are used as the basic unit whereas for the base-pair-step structural parameters, the basic unit is composed of blocks of tetramers. The omega LS-delta G(zero) 10 correlation is the ~~first experimental evidence demonstrating the relationship between the relative local stabilities and the sequence-specific local structures of DNA duplexes~~. ~~It also forms the basis for using the trimer~~-~~tetramer model for the prediction of sequence~~-~~specific local structures of deoxyribonucleic acid molecules.~~		The line below this paragraph, {{ABSTRACT_PUBMED_9102467}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 9102467 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_9102467}}

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

	==Reference==		==Reference==
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	[[Category: Deoxyribonucleic acid]]		[[Category: Deoxyribonucleic acid]]
	[[Category: Dna]]		[[Category: Dna]]
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OCA at 08:58, 2 May 2008

2008-05-02T08:58:12Z

← Older revision		Revision as of 08:58, 2 May 2008
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	[[Image:1buf.jpg\|left\|200px]]		[[Image:1buf.jpg\|left\|200px]]

	~~{{Structure~~		<!--
	~~\|PDB= 1buf \|SIZE=350\|CAPTION= <scene name='initialview01'>1buf~~<~~/scene>~~		The line below this paragraph, containing "STRUCTURE_1buf", creates the "Structure Box" on the page.
	~~\|SITE=~~		You may change the PDB parameter (which sets the PDB file loaded into the applet)
	~~\|LIGAND= <scene name='pdbligand=DA:2'~~-~~DEOXYADENOSINE~~-~~5'-MONOPHOSPHATE'>DA</scene>~~, ~~<scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>~~, <scene ~~name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>~~, ~~<scene name='pdbligand=DT:THYMIDINE~~-~~5'~~-~~MONOPHOSPHATE'>DT</scene~~>		or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
	\|~~ACTIVITY~~=		or leave the SCENE parameter empty for the default display.
	\|~~GENE~~=		-->
	~~\|DOMAIN=~~		{{STRUCTURE_1buf\| PDB=1buf \| SCENE= }}
	~~\|RELATEDENTRY=[[1uqa\|1UQA]], [[1uqb\|1UQB]], [[1uqc\|1UQC]], [[1uqd\|1UQD]], [[1uqe\|1UQE]], [[1uqf\|1UQF]], [[1uqg\|1UQG]]~~
	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1buf OCA], [http://www.ebi.ac.uk/pdbsum/1buf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1buf RCSB]</span>
	}}

	'''SELF-COMPLEMENTARY DNA 5'-D(CAATTG)2, NMR, MINIMIZED AVERAGE STRUCTURE'''		'''SELF-COMPLEMENTARY DNA 5'-D(CAATTG)2, NMR, MINIMIZED AVERAGE STRUCTURE'''
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	==About this Structure==		==About this Structure==
	~~1BUF is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA].		Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUF OCA].

	==Reference==		==Reference==
	Sequence-specific local structural variations in solution structures of d(CGXX'CG)2 and d(CAXX'TG)2 self-complementary deoxyribonucleic acids., Lam SL, Au-Yeung SC, J Mol Biol. 1997 Mar 7;266(4):745-60. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9102467 9102467]		Sequence-specific local structural variations in solution structures of d(CGXX'CG)2 and d(CAXX'TG)2 self-complementary deoxyribonucleic acids., Lam SL, Au-Yeung SC, J Mol Biol. 1997 Mar 7;266(4):745-60. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9102467 9102467]
	~~[[Category: Protein complex]]~~
	[[Category: Au-Yeung, S C.F.]]		[[Category: Au-Yeung, S C.F.]]
	[[Category: Lam, S L.]]		[[Category: Lam, S L.]]
	[[Category: ~~deoxyribonucleic~~ acid]]		[[Category: Deoxyribonucleic acid]]
	[[Category: ~~dna~~]]		[[Category: Dna]]
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