1mv2 - Revision history

OCA at 18:51, 29 November 2023

OCA — Wed, 29 Nov 2023 18:51:28 GMT

←Older revision		Revision as of 18:51, 29 November 2023
Line 1:		Line 1:

	==The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2==		==The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2==
-	<StructureSection load='1mv2' size='340' side='right'caption='[[1mv2~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='1mv2' size='340' side='right'caption='[[1mv2]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1mv2]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MV2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MV2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1mv2]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MV2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MV2 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene~~></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='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1yfv\|1yfv]], [[1gid\|1gid]], [[1muv\|1muv]], [[1mv1\|1mv1]], [[1mv6\|1mv6]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></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=1mv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mv2 OCA], [https://pdbe.org/1mv2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mv2 RCSB], [https://www.ebi.ac.uk/pdbsum/1mv2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mv2 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=1mv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mv2 OCA], [https://pdbe.org/1mv2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mv2 RCSB], [https://www.ebi.ac.uk/pdbsum/1mv2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mv2 ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Burkard~~, M E~~]]	+	[[Category: Burkard ME]]
-	[[Category: Krugh~~, T R~~]]	+	[[Category: Krugh TR]]
-	[[Category: Turner~~, D H~~]]	+	[[Category: Turner DH]]
-	[[Category: Znosko~~, B M]]~~	+	[[Category: Znosko BM]]
-	~~[[Category: Duplex]]~~	+
-	~~[[Category: Purine]]~~	+
-	~~[[Category: Ribonucleic acid]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Tandem mismatch~~]]	+

OCA at 09:30, 5 May 2021

OCA — Wed, 05 May 2021 09:30:02 GMT

←Older revision		Revision as of 09:30, 5 May 2021
Line 3:		Line 3:
	<StructureSection load='1mv2' size='340' side='right'caption='[[1mv2]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1mv2' size='340' side='right'caption='[[1mv2]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1mv2]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MV2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1MV2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1mv2]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MV2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MV2 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yfv\|1yfv]], [[1gid\|1gid]], [[1muv\|1muv]], [[1mv1\|1mv1]], [[1mv6\|1mv6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yfv\|1yfv]], [[1gid\|1gid]], [[1muv\|1muv]], [[1mv1\|1mv1]], [[1mv6\|1mv6]]</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=1mv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mv2 OCA], [~~http~~://pdbe.org/1mv2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1mv2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1mv2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1mv2 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=1mv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mv2 OCA], [https://pdbe.org/1mv2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mv2 RCSB], [https://www.ebi.ac.uk/pdbsum/1mv2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mv2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:22, 31 July 2019

OCA — Wed, 31 Jul 2019 07:22:23 GMT

←Older revision		Revision as of 07:22, 31 July 2019
Line 1:		Line 1:

	==The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2==		==The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2==
-	<StructureSection load='1mv2' size='340' side='right' caption='[[1mv2]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='1mv2' size='340' side='right'caption='[[1mv2]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1mv2]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MV2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MV2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1mv2]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MV2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MV2 FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Burkard, M E]]		[[Category: Burkard, M E]]
	[[Category: Krugh, T R]]		[[Category: Krugh, T R]]

OCA at 10:11, 25 October 2017

OCA — Wed, 25 Oct 2017 10:11:39 GMT

←Older revision		Revision as of 10:11, 25 October 2017
Line 1:		Line 1:
		+
	==The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2==		==The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2==
	<StructureSection load='1mv2' size='340' side='right' caption='[[1mv2]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1mv2' size='340' side='right' caption='[[1mv2]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yfv\|1yfv]], [[1gid\|1gid]], [[1muv\|1muv]], [[1mv1\|1mv1]], [[1mv6\|1mv6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yfv\|1yfv]], [[1gid\|1gid]], [[1muv\|1muv]], [[1mv1\|1mv1]], [[1mv6\|1mv6]]</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=1mv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mv2 OCA], [http://pdbe.org/1mv2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mv2 RCSB], [http://www.ebi.ac.uk/pdbsum/1mv2 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=1mv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mv2 OCA], [http://pdbe.org/1mv2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mv2 RCSB], [http://www.ebi.ac.uk/pdbsum/1mv2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1mv2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:55, 10 September 2015

OCA — Thu, 10 Sep 2015 16:55:15 GMT

←Older revision		Revision as of 16:55, 10 September 2015
Line 5:		Line 5:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yfv\|1yfv]], [[1gid\|1gid]], [[1muv\|1muv]], [[1mv1\|1mv1]], [[1mv6\|1mv6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yfv\|1yfv]], [[1gid\|1gid]], [[1muv\|1muv]], [[1mv1\|1mv1]], [[1mv6\|1mv6]]</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=1mv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mv2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mv2 RCSB], [http://www.ebi.ac.uk/pdbsum/1mv2 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=1mv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mv2 OCA], [http://pdbe.org/1mv2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mv2 RCSB], [http://www.ebi.ac.uk/pdbsum/1mv2 PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 15:
	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 1mv2" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:42, 3 January 2015

OCA — Sat, 03 Jan 2015 22:42:20 GMT

←Older revision		Revision as of 22:42, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1mv2]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MV2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MV2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1mv2]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MV2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MV2 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yfv\|1yfv]], [[1gid\|1gid]], [[1muv\|1muv]], [[1mv1\|1mv1]], [[1mv6\|1mv6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yfv\|1yfv]], [[1gid\|1gid]], [[1muv\|1muv]], [[1mv1\|1mv1]], [[1mv6\|1mv6]]</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=1mv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mv2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mv2 RCSB], [http://www.ebi.ac.uk/pdbsum/1mv2 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=1mv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mv2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mv2 RCSB], [http://www.ebi.ac.uk/pdbsum/1mv2 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 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Burkard, M E.]]	+	[[Category: Burkard, M E]]
-	[[Category: Krugh, T R.]]	+	[[Category: Krugh, T R]]
-	[[Category: Turner, D H.]]	+	[[Category: Turner, D H]]
-	[[Category: Znosko, B M.]]	+	[[Category: Znosko, B M]]
	[[Category: Duplex]]		[[Category: Duplex]]
	[[Category: Purine]]		[[Category: Purine]]

OCA at 06:51, 9 June 2014

OCA — Mon, 09 Jun 2014 06:51:00 GMT

←Older revision		Revision as of 06:51, 9 June 2014
Line 1:		Line 1:
-	[[~~Image:~~1mv2.~~png~~\|~~left~~\|~~200px~~]]	+	==The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2==
		+	<StructureSection load='1mv2' size='340' side='right' caption='[[1mv2]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1mv2]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MV2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MV2 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yfv\|1yfv]], [[1gid\|1gid]], [[1muv\|1muv]], [[1mv1\|1mv1]], [[1mv6\|1mv6]]</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=1mv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mv2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mv2 RCSB], [http://www.ebi.ac.uk/pdbsum/1mv2 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The contribution of amino groups to the thermodynamics, structure, and dynamics of tandem A.A mismatches is investigated by substitution of purine (P) for adenine (A) within the RNA duplex, 5'(rGGCAAGCCU)(2), to give 5'(rGGCPAGCCU)(2), 5'(rGGCAPGCCU)(2), and 5'(rGGCPPGCCU)(2). The 5'(rGGCAAGCCU)(2) duplex has sheared A(anti).A(anti) (A.A trans Hoogsteen/Sugar-edge) pairs in which the A5 amino group is involved in hydrogen bonds but the A4 amino group is not [Znosko, B. M., Burkard, M. E., Schroeder, S. J., Krugh, T. R., and Turner, D. H. (2002) Biochemistry 41, 14969-14977]. In comparison to 5'(rGGCAAGCCU)(2), replacing the amino group of A4 with a hydrogen stabilizes the duplex by 1.3 kcal/mol, replacement of the A5 amino group destabilizes the duplex by 0.6 kcal/mol, and replacement of both A4 and A5 amino groups destabilizes the duplex by 0.8 kcal/mol. In NMR structures, the P.A noncanonical pairs of the 5'(rGGCPAGCCU)(2) duplex have a sheared anti-anti structure (P.A trans Hoogsteen/Sugar-edge) with P4.A5 interstrand hydrogen bonding and A5 bases that interstrand stack, similar to the structure of 5'(rGGCAAGCCU)(2). In contrast, the A.P pairs of the 5'(rGGCAPGCCU)(2) duplex have a face-to-face conformation (A.P trans Watson-Crick/Watson-Crick) with intrastrand stacking resembling typical A-form geometry. Although the P5 bases in 5'(rGGCPPGCCU)(2) are involved in an interstrand stack, the loop region is largely undefined. The results illustrate that both hydrogen-bonded and non-hydrogen-bonded amino groups play important roles in determining the thermodynamic, structural, and dynamic characteristics of purine rich internal loops.

-	~~{{STRUCTURE_1mv2\| PDB=1mv2 \| SCENE= }}~~	+	Molecular recognition in purine-rich internal loops: thermodynamic, structural, and dynamic consequences of purine for adenine substitutions in 5'(rGGCAAGCCU)2.,Znosko BM, Burkard ME, Krugh TR, Turner DH Biochemistry. 2002 Dec 17;41(50):14978-87. PMID:12475247<ref>PMID:12475247</ref>

-	~~===The tandem~~, ~~Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12475247}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1mv2]] is~~ a ~~2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1MV2 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012475247<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Burkard, M E.]]		[[Category: Burkard, M E.]]
	[[Category: Krugh, T R.]]		[[Category: Krugh, T R.]]

OCA: Protected "1mv2" [edit=sysop:move=sysop]

OCA — Tue, 14 Aug 2012 17:33:54 GMT

Protected "1mv2" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:33, 14 August 2012

OCA at 17:33, 14 August 2012

OCA — Tue, 14 Aug 2012 17:33:52 GMT

←Older revision		Revision as of 17:33, 14 August 2012
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-	{{Seed}}
	[[Image:1mv2.png\|left\|200px]]		[[Image:1mv2.png\|left\|200px]]

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	{{STRUCTURE_1mv2\| PDB=1mv2 \| SCENE= }}		{{STRUCTURE_1mv2\| PDB=1mv2 \| SCENE= }}

	===The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2===		===The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2===

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-	(as it appears on PubMed at http://www.pubmed.gov), where 12475247 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_12475247}}		{{ABSTRACT_PUBMED_12475247}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MV2 OCA].	+	[[1mv2]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MV2 OCA].

	==Reference==		==Reference==
-	Molecular recognition in purine-rich internal loops: thermodynamic, structural, and dynamic consequences of purine for adenine substitutions in 5'(rGGCAAGCCU)2., Znosko BM, Burkard ME, Krugh TR, Turner DH, Biochemistry. 2002 Dec 17;41(50):14978-87. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~12475247 12475247]~~	+	<ref group="xtra">PMID:012475247</ref><references group="xtra"/>
	[[Category: Burkard, M E.]]		[[Category: Burkard, M E.]]
	[[Category: Krugh, T R.]]		[[Category: Krugh, T R.]]
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	[[Category: Purine]]		[[Category: Purine]]
	[[Category: Ribonucleic acid]]		[[Category: Ribonucleic acid]]
		+	[[Category: Rna]]
	[[Category: Tandem mismatch]]		[[Category: Tandem mismatch]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 08:21:06 2008''

OCA at 05:21, 28 July 2008

OCA — Mon, 28 Jul 2008 05:21:12 GMT

←Older revision		Revision as of 05:21, 28 July 2008
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-	[[Image:1mv2.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1mv2.png\|left\|200px]]

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	{{STRUCTURE_1mv2\| PDB=1mv2 \| SCENE= }}		{{STRUCTURE_1mv2\| PDB=1mv2 \| SCENE= }}

-	~~'''~~The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2~~'''~~	+	===The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2===


-	~~==Overview==~~	+	<!--
-	The ~~contribution of amino groups to the thermodynamics~~, ~~structure~~, ~~and dynamics of tandem A.A mismatches is investigated by substitution of purine (P) for adenine (A) within~~ the ~~RNA duplex, 5'(rGGCAAGCCU)(2),~~ to ~~give 5'(rGGCPAGCCU)(2), 5'(rGGCAPGCCU)(2), and 5'(rGGCPPGCCU)(2). The 5'(rGGCAAGCCU)(2) duplex has sheared A(anti).A(anti) (A.A trans Hoogsteen/Sugar-edge) pairs in which~~ the ~~A5 amino group is involved in hydrogen bonds but the A4 amino group is not [Znosko, B. M., Burkard, M. E., Schroeder, S. J., Krugh, T. R., and Turner, D. H.~~ (~~2002) Biochemistry 41, 14969-14977]. In comparison to 5'(rGGCAAGCCU)(2), replacing the amino group of A4 with a hydrogen stabilizes the duplex by 1.3 kcal~~/~~mol, replacement of the A5 amino group destabilizes the duplex by 0.6 kcal~~/~~mol, and replacement of both A4 and A5 amino groups destabilizes the duplex by 0~~.~~8 kcal/mol~~. ~~In NMR structures, the P.A noncanonical pairs of the 5'(rGGCPAGCCU~~)~~(2) duplex have a sheared anti-anti structure (P.A trans Hoogsteen/Sugar-edge) with P4.A5 interstrand hydrogen bonding and A5 bases that interstrand stack~~, ~~similar to~~ the ~~structure of 5'(rGGCAAGCCU)(2)~~. ~~In contrast, the A.P pairs of the 5'(rGGCAPGCCU)(2) duplex have a face~~-to-face conformation (A.P trans Watson-Crick/Watson-Crick) with intrastrand stacking resembling typical A-form geometry. Although the P5 bases in 5'(rGGCPPGCCU)(2) are involved in an interstrand stack, the loop region is largely undefined. The results illustrate that both hydrogen-bonded and non-hydrogen-bonded amino groups play important roles in determining the thermodynamic, structural, and dynamic characteristics of purine rich internal loops.	+	The line below this paragraph, {{ABSTRACT_PUBMED_12475247}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 12475247 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_12475247}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MV2 OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MV2 OCA].

	==Reference==		==Reference==
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	[[Category: Ribonucleic acid]]		[[Category: Ribonucleic acid]]
	[[Category: Tandem mismatch]]		[[Category: Tandem mismatch]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 01:45~~:21 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 08:21:06 2008''