1rrd - Revision history

OCA at 09:22, 6 December 2023

OCA — Wed, 06 Dec 2023 09:22:03 GMT

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

	==DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10 STRUCTURES==		==DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10 STRUCTURES==
-	<StructureSection load='1rrd' size='340' side='right'caption='[[1rrd~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>	+	<StructureSection load='1rrd' size='340' side='right'caption='[[1rrd]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rrd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RRD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rrd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RRD FirstGlance]. <br>
-	</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=1rrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrd OCA], [https://pdbe.org/1rrd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rrd RCSB], [https://www.ebi.ac.uk/pdbsum/1rrd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rrd ProSAT]</span></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=1rrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrd OCA], [https://pdbe.org/1rrd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rrd RCSB], [https://www.ebi.ac.uk/pdbsum/1rrd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rrd ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brown, T]]	+	[[Category: Brown T]]
-	[[Category: Conn~~, G L~~]]	+	[[Category: Conn GL]]
-	[[Category: Gyi~~, J I~~]]	+	[[Category: Gyi JI]]
-	[[Category: Lane~~, A N]]~~	+	[[Category: Lane AN]]
-	~~[[Category: Antisense]]~~	+
-	~~[[Category: Dna-rna hybrid]]~~	+
-	~~[[Category: Dna/rna hybrid]]~~	+
-	~~[[Category: Purine/pyrimidine-rich strand~~]]	+

OCA at 07:20, 22 September 2021

OCA — Wed, 22 Sep 2021 07:20:41 GMT

←Older revision		Revision as of 07:20, 22 September 2021
Line 3:		Line 3:
	<StructureSection load='1rrd' size='340' side='right'caption='[[1rrd]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1rrd' size='340' side='right'caption='[[1rrd]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rrd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1RRD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rrd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RRD FirstGlance]. <br>
-	</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=1rrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrd OCA], [~~http~~://pdbe.org/1rrd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1rrd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1rrd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1rrd ProSAT]</span></td></tr>	+	</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=1rrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrd OCA], [https://pdbe.org/1rrd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rrd RCSB], [https://www.ebi.ac.uk/pdbsum/1rrd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rrd ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:40, 11 December 2019

OCA — Wed, 11 Dec 2019 19:40:33 GMT

←Older revision		Revision as of 19:40, 11 December 2019
Line 1:		Line 1:

	==DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10 STRUCTURES==		==DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10 STRUCTURES==
-	<StructureSection load='1rrd' size='340' side='right' caption='[[1rrd]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>	+	<StructureSection load='1rrd' size='340' side='right'caption='[[1rrd]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rrd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RRD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rrd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RRD FirstGlance]. <br>
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Brown, T]]		[[Category: Brown, T]]
	[[Category: Conn, G L]]		[[Category: Conn, G L]]

OCA at 07:10, 8 March 2018

OCA — Thu, 08 Mar 2018 07:10:59 GMT

←Older revision		Revision as of 07:10, 8 March 2018
Line 1:		Line 1:
		+
	==DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10 STRUCTURES==		==DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10 STRUCTURES==
	<StructureSection load='1rrd' size='340' side='right' caption='[[1rrd]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1rrd' size='340' side='right' caption='[[1rrd]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rrd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RRD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rrd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RRD FirstGlance]. <br>
-	</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=1rrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrd OCA], [http://pdbe.org/1rrd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rrd RCSB], [http://www.ebi.ac.uk/pdbsum/1rrd PDBsum]</span></td></tr>	+	</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=1rrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrd OCA], [http://pdbe.org/1rrd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rrd RCSB], [http://www.ebi.ac.uk/pdbsum/1rrd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rrd ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:06, 11 September 2015

OCA — Fri, 11 Sep 2015 17:06:46 GMT

←Older revision		Revision as of 17:06, 11 September 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rrd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RRD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rrd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RRD FirstGlance]. <br>
-	</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=1rrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rrd RCSB], [http://www.ebi.ac.uk/pdbsum/1rrd PDBsum]</span></td></tr>	+	</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=1rrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrd OCA], [http://pdbe.org/1rrd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rrd RCSB], [http://www.ebi.ac.uk/pdbsum/1rrd PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 13:		Line 13:
	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 1rrd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:04, 3 January 2015

OCA — Sat, 03 Jan 2015 22:04:33 GMT

←Older revision		Revision as of 22:04, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rrd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RRD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rrd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RRD FirstGlance]. <br>
-	</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=1rrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rrd RCSB], [http://www.ebi.ac.uk/pdbsum/1rrd PDBsum]</span></td></tr>	+	</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=1rrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rrd RCSB], [http://www.ebi.ac.uk/pdbsum/1rrd 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 17:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Brown, T.]]	+	[[Category: Brown, T]]
-	[[Category: Conn, G L.]]	+	[[Category: Conn, G L]]
-	[[Category: Gyi, J I.]]	+	[[Category: Gyi, J I]]
-	[[Category: Lane, A N.]]	+	[[Category: Lane, A N]]
	[[Category: Antisense]]		[[Category: Antisense]]
	[[Category: Dna-rna hybrid]]		[[Category: Dna-rna hybrid]]
	[[Category: Dna/rna hybrid]]		[[Category: Dna/rna hybrid]]
	[[Category: Purine/pyrimidine-rich strand]]		[[Category: Purine/pyrimidine-rich strand]]

OCA at 07:09, 9 June 2014

OCA — Mon, 09 Jun 2014 07:09:13 GMT

←Older revision		Revision as of 07:09, 9 June 2014
Line 1:		Line 1:
-	[[~~Image~~:1rrd.~~png\|left\|200px~~]]	+	==DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10 STRUCTURES==
		+	<StructureSection load='1rrd' size='340' side='right' caption='[[1rrd]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1rrd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RRD FirstGlance]. <br>
		+	</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=1rrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rrd RCSB], [http://www.ebi.ac.uk/pdbsum/1rrd PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The structures of d(GAAGAGAAGC).d(GCTTCTCTTC), d(GAAGAGAAGC). r(GCUUCUCUUC), r(GAAGAGAAGC).d(GCTTCTCTTC), and r(GAAGAGAAGC). r(GCUUCUCUUC) have been determined in solution from NMR data. Globally, the pure DNA and RNA duplexes were in the B and A forms, respectively. The two DNA.RNA hybrids were neither A nor B, but closer globally to the A than the B form. However, the thermodynamically less stable d(GAAGAGAAGC).r(GCUUCUCUUC) duplex has a significantly different conformation from r(GAAGAGAAGC). d(GCTTCTCTTC). Structures were calculated based on the NMR data, using restrained molecular dynamics. A new approach to the treatment of conformational averaging based on a prioriprobabilities has been used. The nucleotides were treated by fitting the scalar coupling data and NOE time courses to a two-state model comprising N and S sugar puckers each with a different glycosidic torsion angle, and the mole fraction of the S state. Restraint sets for different distributions of N and S states within molecules were constructed, such that each nucleotide was weighted in the ensemble according to the mole fractions (or a prioriprobabilities). The individual nucleotide conformations were strongly restrained, whereas the internucleotide restraints were set relatively loosely. Ensembles of conformations were generated and assessed by comparison of the NOEs calculated from ensemble-averaged relaxation matrices with the experimental NOEs. The ensemble averages accounted for the experimental data much better than any individual member, or for structures calculated assuming a single unique conformation. The two hybrids populated different degrees of conformational space. There was a general trend in minor and major groove widths in the order d(GAAGAGAAGC).d(GCTTCTCTTC), d(GAAGAGAAGC).r(GCUUCUCUUC), r(GAAGAGAAGC).d(GCTTCTCTTC), r(GAAGAGAAGC).r(GCUUCUCUUC) and a similar progression in global character from B-like to A-like structures. Furthermore, r(GAAGAGAAGC).d(GCTTCTCTTC) showed a greater dispersion of conformations in the ensemble than d(GAAGAGAAGC).r(GCUUCUCUUC), reflecting the greater flexibility of the sugars. If conformational averaging of the nucleotides is ignored, incorrect virtual structures are produced that nevertheless are able to satisfy a substantial fraction of the experimental data.

-	~~{{STRUCTURE_1rrd\| PDB=1rrd \| SCENE= }}~~	+	Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes.,Gyi JI, Lane AN, Conn GL, Brown T Biochemistry. 1998 Jan 6;37(1):73-80. PMID:9425027<ref>PMID:9425027</ref>

-	~~===DNA~~/~~RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND~~, ~~NMR, 10 STRUCTURES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9425027}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1rrd]] is~~ a ~~2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1RRD OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:009425027<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Brown, T.]]		[[Category: Brown, T.]]
	[[Category: Conn, G L.]]		[[Category: Conn, G L.]]

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

OCA — Tue, 14 Aug 2012 16:33:16 GMT

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

←Older revision

Revision as of 16:33, 14 August 2012

OCA at 16:33, 14 August 2012

OCA — Tue, 14 Aug 2012 16:33:15 GMT

←Older revision		Revision as of 16:33, 14 August 2012
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-	{{Seed}}
	[[Image:1rrd.png\|left\|200px]]		[[Image:1rrd.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_1rrd\| PDB=1rrd \| SCENE= }}		{{STRUCTURE_1rrd\| PDB=1rrd \| SCENE= }}

	===DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10 STRUCTURES===		===DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10 STRUCTURES===

-
-	<!--
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	{{ABSTRACT_PUBMED_9425027}}		{{ABSTRACT_PUBMED_9425027}}

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

	==Reference==		==Reference==
-	Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes., Gyi JI, Lane AN, Conn GL, Brown T, Biochemistry. 1998 Jan 6;37(1):73-80. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~9425027 9425027]~~	+	<ref group="xtra">PMID:009425027</ref><references group="xtra"/>
	[[Category: Brown, T.]]		[[Category: Brown, T.]]
	[[Category: Conn, G L.]]		[[Category: Conn, G L.]]
Line 29:		Line 17:
	[[Category: Lane, A N.]]		[[Category: Lane, A N.]]
	[[Category: Antisense]]		[[Category: Antisense]]
		+	[[Category: Dna-rna hybrid]]
	[[Category: Dna/rna hybrid]]		[[Category: Dna/rna hybrid]]
	[[Category: Purine/pyrimidine-rich strand]]		[[Category: Purine/pyrimidine-rich strand]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 11:06:06 2008''

OCA at 08:06, 29 July 2008

OCA — Tue, 29 Jul 2008 08:06:23 GMT

←Older revision		Revision as of 08:06, 29 July 2008
Line 1:		Line 1:
-	[[Image:1rrd.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1rrd.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1rrd\| PDB=1rrd \| SCENE= }}		{{STRUCTURE_1rrd\| PDB=1rrd \| SCENE= }}

-	~~'''~~DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10 STRUCTURES~~'''~~	+	===DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10 STRUCTURES===


-	~~==Overview==~~	+	<!--
-	The ~~structures of d(GAAGAGAAGC).d(GCTTCTCTTC)~~, ~~d(GAAGAGAAGC). r(GCUUCUCUUC), r(GAAGAGAAGC).d(GCTTCTCTTC), and r(GAAGAGAAGC). r(GCUUCUCUUC) have been determined in solution from NMR data. Globally~~, the ~~pure DNA and RNA duplexes were in the B and A forms, respectively. The two DNA.RNA hybrids were neither A nor B, but closer globally~~ to the ~~A than the B form. However, the thermodynamically less stable d~~(~~GAAGAGAAGC).r(GCUUCUCUUC) duplex has a significantly different conformation from r(GAAGAGAAGC). d(GCTTCTCTTC). Structures were calculated based~~ on ~~the NMR data, using restrained molecular dynamics~~. ~~A new approach to the treatment of conformational averaging based on a prioriprobabilities has been used~~. The nucleotides were treated by fitting the scalar coupling data and NOE time courses to a two-state model comprising N and S sugar puckers each with a different glycosidic torsion angle, and the mole fraction of the S state. Restraint sets for different distributions of N and S states within molecules were constructed, such that each nucleotide was weighted in the ensemble according to the mole fractions (or a prioriprobabilities)~~. The individual nucleotide conformations were strongly restrained~~, ~~whereas~~ the ~~internucleotide restraints were set relatively loosely~~. ~~Ensembles of conformations were generated and assessed by comparison of the NOEs calculated from ensemble~~-averaged relaxation matrices with the experimental NOEs. The ensemble averages accounted for the experimental data much better than any individual member, or for structures calculated assuming a single unique conformation. The two hybrids populated different degrees of conformational space. There was a general trend in minor and major groove widths in the order d(GAAGAGAAGC).d(GCTTCTCTTC), d(GAAGAGAAGC).r(GCUUCUCUUC), r(GAAGAGAAGC).d(GCTTCTCTTC), r(GAAGAGAAGC).r(GCUUCUCUUC) and a similar progression in global character from B-like to A-like structures. Furthermore, r(GAAGAGAAGC).d(GCTTCTCTTC) showed a greater dispersion of conformations in the ensemble than d(GAAGAGAAGC).r(GCUUCUCUUC), reflecting the greater flexibility of the sugars. If conformational averaging of the nucleotides is ignored, incorrect virtual structures are produced that nevertheless are able to satisfy a substantial fraction of the experimental data.	+	The line below this paragraph, {{ABSTRACT_PUBMED_9425027}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9425027 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9425027}}

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

	==Reference==		==Reference==
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	[[Category: Dna/rna hybrid]]		[[Category: Dna/rna hybrid]]
	[[Category: Purine/pyrimidine-rich strand]]		[[Category: Purine/pyrimidine-rich strand]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 07~~:49:17 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 11:06:06 2008''