1k1r - Revision history

OCA at 18:45, 29 November 2023

OCA — Wed, 29 Nov 2023 18:45:04 GMT

←Older revision		Revision as of 18:45, 29 November 2023
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	==HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX==		==HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX==
-	<StructureSection load='1k1r' size='340' side='right'caption='[[1k1r~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='1k1r' size='340' side='right'caption='[[1k1r]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1k1r]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K1R FirstGlance]. <br>		<table><tr><td colspan='2'>[[1k1r]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K1R FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CMR:2-DEOXY-CYTIDINE-5-RP-MONOMETHYLPHOSPHONATE'>CMR</scene>, <scene name='pdbligand=RMP:2-DEOXY-ADENOSINE-5-RP-MONOMETHYLPHOSPHONATE'>RMP</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;~~'>~~[[1k1h\|1k1h]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMR:2-DEOXY-CYTIDINE-5-RP-MONOMETHYLPHOSPHONATE'>CMR</scene>, <scene name='pdbligand=RMP:2-DEOXY-ADENOSINE-5-RP-MONOMETHYLPHOSPHONATE'>RMP</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=1k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1r OCA], [https://pdbe.org/1k1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k1r RCSB], [https://www.ebi.ac.uk/pdbsum/1k1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k1r 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=1k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1r OCA], [https://pdbe.org/1k1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k1r RCSB], [https://www.ebi.ac.uk/pdbsum/1k1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k1r ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Abramova~~, T V~~]]	+	[[Category: Abramova TV]]
-	[[Category: Bichenkova, E]]	+	[[Category: Bichenkova E]]
-	[[Category: Gorenstein~~, D G~~]]	+	[[Category: Gorenstein DG]]
-	[[Category: Gozansky~~, E K~~]]	+	[[Category: Gozansky EK]]
-	[[Category: Lebedev~~, A V~~]]	+	[[Category: Lebedev AV]]
-	[[Category: Luxon~~, B A~~]]	+	[[Category: Luxon BA]]
-	[[Category: Thiviyanathan, V]]	+	[[Category: Thiviyanathan V]]
-	[[Category: Vyazovkina~~, K V]]~~	+	[[Category: Vyazovkina KV]]
-	~~[[Category: Anti sense]]~~	+
-	~~[[Category: Aptamer]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Methyl phosphonate]]~~	+
-	~~[[Category: Modified dna~~]]	+

OCA at 08:44, 21 April 2021

OCA — Wed, 21 Apr 2021 08:44:54 GMT

←Older revision		Revision as of 08:44, 21 April 2021
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	<StructureSection load='1k1r' size='340' side='right'caption='[[1k1r]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1k1r' size='340' side='right'caption='[[1k1r]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k1r]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1K1R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k1r]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K1R FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMR:2-DEOXY-CYTIDINE-5-RP-MONOMETHYLPHOSPHONATE'>CMR</scene>, <scene name='pdbligand=RMP:2-DEOXY-ADENOSINE-5-RP-MONOMETHYLPHOSPHONATE'>RMP</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=CMR:2-DEOXY-CYTIDINE-5-RP-MONOMETHYLPHOSPHONATE'>CMR</scene>, <scene name='pdbligand=RMP:2-DEOXY-ADENOSINE-5-RP-MONOMETHYLPHOSPHONATE'>RMP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k1h\|1k1h]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1k1h\|1k1h]]</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=1k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1r OCA], [~~http~~://pdbe.org/1k1r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1k1r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1k1r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1k1r 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=1k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1r OCA], [https://pdbe.org/1k1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k1r RCSB], [https://www.ebi.ac.uk/pdbsum/1k1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k1r ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:36, 17 July 2019

OCA — Wed, 17 Jul 2019 13:36:09 GMT

←Older revision		Revision as of 13:36, 17 July 2019
Line 1:		Line 1:

	==HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX==		==HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX==
-	<StructureSection load='1k1r' size='340' side='right' caption='[[1k1r]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='1k1r' size='340' side='right'caption='[[1k1r]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1k1r]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K1R FirstGlance]. <br>		<table><tr><td colspan='2'>[[1k1r]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K1R FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Abramova, T V]]		[[Category: Abramova, T V]]
	[[Category: Bichenkova, E]]		[[Category: Bichenkova, E]]

OCA at 07:25, 11 October 2017

OCA — Wed, 11 Oct 2017 07:25:16 GMT

←Older revision		Revision as of 07:25, 11 October 2017
Line 1:		Line 1:
		+
	==HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX==		==HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX==
	<StructureSection load='1k1r' size='340' side='right' caption='[[1k1r]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1k1r' size='340' side='right' caption='[[1k1r]], [[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=CMR:2-DEOXY-CYTIDINE-5-RP-MONOMETHYLPHOSPHONATE'>CMR</scene>, <scene name='pdbligand=RMP:2-DEOXY-ADENOSINE-5-RP-MONOMETHYLPHOSPHONATE'>RMP</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=CMR:2-DEOXY-CYTIDINE-5-RP-MONOMETHYLPHOSPHONATE'>CMR</scene>, <scene name='pdbligand=RMP:2-DEOXY-ADENOSINE-5-RP-MONOMETHYLPHOSPHONATE'>RMP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k1h\|1k1h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k1h\|1k1h]]</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=1k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1r OCA], [http://pdbe.org/1k1r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k1r RCSB], [http://www.ebi.ac.uk/pdbsum/1k1r 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=1k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1r OCA], [http://pdbe.org/1k1r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k1r RCSB], [http://www.ebi.ac.uk/pdbsum/1k1r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k1r ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:01, 11 September 2015

OCA — Fri, 11 Sep 2015 05:01:36 GMT

←Older revision		Revision as of 05:01, 11 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=CMR:2-DEOXY-CYTIDINE-5-RP-MONOMETHYLPHOSPHONATE'>CMR</scene>, <scene name='pdbligand=RMP:2-DEOXY-ADENOSINE-5-RP-MONOMETHYLPHOSPHONATE'>RMP</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=CMR:2-DEOXY-CYTIDINE-5-RP-MONOMETHYLPHOSPHONATE'>CMR</scene>, <scene name='pdbligand=RMP:2-DEOXY-ADENOSINE-5-RP-MONOMETHYLPHOSPHONATE'>RMP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k1h\|1k1h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k1h\|1k1h]]</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=1k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k1r RCSB], [http://www.ebi.ac.uk/pdbsum/1k1r 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=1k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1r OCA], [http://pdbe.org/1k1r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k1r RCSB], [http://www.ebi.ac.uk/pdbsum/1k1r 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 1k1r" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:04, 3 January 2015

OCA — Sat, 03 Jan 2015 22:04:50 GMT

←Older revision		Revision as of 22:04, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1k1r]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K1R FirstGlance]. <br>		<table><tr><td colspan='2'>[[1k1r]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K1R FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMR:2-DEOXY-CYTIDINE-5-RP-MONOMETHYLPHOSPHONATE'>CMR</scene>, <scene name='pdbligand=RMP:2-DEOXY-ADENOSINE-5-RP-MONOMETHYLPHOSPHONATE'>RMP</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=CMR:2-DEOXY-CYTIDINE-5-RP-MONOMETHYLPHOSPHONATE'>CMR</scene>, <scene name='pdbligand=RMP:2-DEOXY-ADENOSINE-5-RP-MONOMETHYLPHOSPHONATE'>RMP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k1h\|1k1h]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k1h\|1k1h]]</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=1k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k1r RCSB], [http://www.ebi.ac.uk/pdbsum/1k1r 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=1k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k1r RCSB], [http://www.ebi.ac.uk/pdbsum/1k1r 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: Abramova, T V.]]	+	[[Category: Abramova, T V]]
-	[[Category: Bichenkova, E.]]	+	[[Category: Bichenkova, E]]
-	[[Category: Gorenstein, D G.]]	+	[[Category: Gorenstein, D G]]
-	[[Category: Gozansky, E K.]]	+	[[Category: Gozansky, E K]]
-	[[Category: Lebedev, A V.]]	+	[[Category: Lebedev, A V]]
-	[[Category: Luxon, B A.]]	+	[[Category: Luxon, B A]]
-	[[Category: Thiviyanathan, V.]]	+	[[Category: Thiviyanathan, V]]
-	[[Category: Vyazovkina, K V.]]	+	[[Category: Vyazovkina, K V]]
	[[Category: Anti sense]]		[[Category: Anti sense]]
	[[Category: Aptamer]]		[[Category: Aptamer]]

OCA at 05:46, 8 June 2014

OCA — Sun, 08 Jun 2014 05:46:55 GMT

←Older revision		Revision as of 05:46, 8 June 2014
Line 1:		Line 1:
-	[[~~Image:~~1k1r.~~png~~\|~~left~~\|~~200px~~]]	+	==HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX==
		+	<StructureSection load='1k1r' size='340' side='right' caption='[[1k1r]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1k1r]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K1R FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMR:2-DEOXY-CYTIDINE-5-RP-MONOMETHYLPHOSPHONATE'>CMR</scene>, <scene name='pdbligand=RMP:2-DEOXY-ADENOSINE-5-RP-MONOMETHYLPHOSPHONATE'>RMP</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1k1h\|1k1h]]</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=1k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k1r RCSB], [http://www.ebi.ac.uk/pdbsum/1k1r PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methyl phosphonate oligonucleotides have been used as antisense and antigene agents. Substitution of a methyl group for oxygen in the phosphate ester backbone introduces a new chiral center. Significant differences in physical properties and hybridization abilities are observed between the R(p) and S(p) diastereomers. Chirally pure methylphosphonate deoxyribooligonucleotides were synthesized, and the solution structures of duplexes formed between a single strand heptanucleotide methylphosphonate, d(Cp(Me)Cp(Me)Ap(Me)Ap(Me)Ap(Me)Cp(Me)A), hybridized to a complementary octanucleotide, d(TpGpTpTpTpGpGpC), were studied by NMR spectroscopy. Stereochemistry at the methylphosphonate center for the heptanucleotide was either RpRpRpRpRpRp (R(p) stereoisomer) or RpRpRpSpRpRp (S(p) stereoisomer, although only one of the six methylphosphonate centers has the S(p) stereochemistry). The results show that the methylphosphonate strands in the heteroduplexes exhibit increased dynamics relative to the DNA strand. Substitution of one chiral center from R(p) to S(p) has a profound effect on the hybridization ability of the methylphosphonate strand. Sugars in the phosphodiester strand exhibit C(2)(') endo sugar puckering while the sugars in the methyl phosphonate strand exhibit an intermediate C(4)(') endo puckering. Bases are well stacked on each other throughout the duplex. The hybridization of the methylphosphonate strand does not perturb the structure of the complementary DNA strand in the hetero duplexes. The sugar residue 5' to the S(p) chiral center shows A-form sugar puckering, with a C(3)(')-endo conformation. Minor groove width in the R(p) stereoisomer is considerably wider, particularly at the R(p) vs S(p) site and is attributed to either steric interactions across the minor groove or poorer metal ion coordination within the minor groove.

-	~~{{STRUCTURE_1k1r\| PDB=1k1r \| SCENE= }}~~	+	Structure of hybrid backbone methylphosphonate DNA heteroduplexes: effect of R and S stereochemistry.,Thiviyanathan V, Vyazovkina KV, Gozansky EK, Bichenchova E, Abramova TV, Luxon BA, Lebedev AV, Gorenstein DG Biochemistry. 2002 Jan 22;41(3):827-38. PMID:11790104<ref>PMID:11790104</ref>

-	~~===HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE~~/~~DNA DUPLEX===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11790104}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1k1r]] is~~ a ~~2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1K1R OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011790104<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Abramova, T V.]]		[[Category: Abramova, T V.]]
	[[Category: Bichenkova, E.]]		[[Category: Bichenkova, E.]]

OCA: Protected "1k1r" [edit=sysop:move=sysop]

OCA — Tue, 14 Aug 2012 16:33:52 GMT

Protected "1k1r" [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 16:33:50 GMT

←Older revision		Revision as of 16:33, 14 August 2012
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-	{{Seed}}
	[[Image:1k1r.png\|left\|200px]]		[[Image:1k1r.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1k1r", 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_1k1r\| PDB=1k1r \| SCENE= }}		{{STRUCTURE_1k1r\| PDB=1k1r \| SCENE= }}

	===HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX===		===HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11790104}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11790104 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11790104}}		{{ABSTRACT_PUBMED_11790104}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1R OCA].	+	[[1k1r]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1R OCA].

	==Reference==		==Reference==
-	Structure of hybrid backbone methylphosphonate DNA heteroduplexes: effect of R and S stereochemistry., Thiviyanathan V, Vyazovkina KV, Gozansky EK, Bichenchova E, Abramova TV, Luxon BA, Lebedev AV, Gorenstein DG, Biochemistry. 2002 Jan 22;41(3):827-38. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~11790104 11790104]~~	+	<ref group="xtra">PMID:011790104</ref><references group="xtra"/>
	[[Category: Abramova, T V.]]		[[Category: Abramova, T V.]]
	[[Category: Bichenkova, E.]]		[[Category: Bichenkova, E.]]
Line 34:		Line 22:
	[[Category: Anti sense]]		[[Category: Anti sense]]
	[[Category: Aptamer]]		[[Category: Aptamer]]
		+	[[Category: Dna]]
	[[Category: Methyl phosphonate]]		[[Category: Methyl phosphonate]]
	[[Category: Modified dna]]		[[Category: Modified dna]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 21:18:54 2008''

OCA at 18:18, 1 July 2008

OCA — Tue, 01 Jul 2008 18:18:58 GMT

←Older revision		Revision as of 18:18, 1 July 2008
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-	[[Image:1k1r.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1k1r.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1k1r\| PDB=1k1r \| SCENE= }}		{{STRUCTURE_1k1r\| PDB=1k1r \| SCENE= }}

-	~~'''~~HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX~~'''~~	+	===HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX===


-	~~==Overview==~~	+	<!--
-	Methyl phosphonate oligonucleotides have been used as antisense and antigene agents. Substitution of a methyl group for oxygen in the phosphate ester backbone introduces a new chiral center. Significant differences in physical properties and hybridization abilities are observed between the R(p) and S(p) diastereomers. Chirally pure methylphosphonate deoxyribooligonucleotides were synthesized, ~~and the solution structures of duplexes formed between a single strand heptanucleotide methylphosphonate~~, ~~d(Cp(Me)Cp(Me)Ap(Me)Ap(Me)Ap(Me)Cp(Me)A), hybridized to a complementary octanucleotide, d(TpGpTpTpTpGpGpC), were studied by NMR spectroscopy. Stereochemistry at~~ the methylphosphonate center for the heptanucleotide was either RpRpRpRpRpRp (R(p) stereoisomer) or RpRpRpSpRpRp (S(p) stereoisomer, although only one of the six methylphosphonate centers has the S(p) stereochemistry). The results show that the methylphosphonate strands in the heteroduplexes exhibit increased dynamics relative to the ~~DNA strand. Substitution of one chiral center from R~~(~~p) to S(p) has a profound effect~~ on ~~the hybridization ability of the methylphosphonate strand~~. ~~Sugars in the phosphodiester strand exhibit C(2)(') endo sugar puckering while the sugars in the methyl phosphonate strand exhibit an intermediate C(4)(') endo puckering~~. Bases are well stacked on each other throughout the duplex. The hybridization of the methylphosphonate strand does not perturb the structure of the complementary DNA strand in the hetero duplexes. The sugar residue 5' to the S(p) ~~chiral center shows A-form sugar puckering~~, ~~with a C(3)(')-endo conformation. Minor groove width in the R(p) stereoisomer~~ is ~~considerably wider, particularly at~~ the ~~R(p) vs S(p) site and is attributed to either steric interactions across the minor groove or poorer metal ion coordination within the minor groove~~.	+	The line below this paragraph, {{ABSTRACT_PUBMED_11790104}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 11790104 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_11790104}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1R OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1R OCA].

	==Reference==		==Reference==
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	[[Category: Methyl phosphonate]]		[[Category: Methyl phosphonate]]
	[[Category: Modified dna]]		[[Category: Modified dna]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May~~ ~~2 22~~:11:33 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 21:18:54 2008''