2dpc - Revision history

OCA at 18:43, 20 September 2023

2023-09-20T18:43:17Z

← Older revision		Revision as of 18:43, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dpc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DPC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dpc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DPC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMY:(6-AMINOHEXYL)CARBAMIC+ACID'>CMY</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>~~		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.55Å</td></tr>
	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene~~></td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMY:(6-AMINOHEXYL)CARBAMIC+ACID'>CMY</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dp7\|2dp7]], [[2dpb\|2dpb]]</div~~></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=2dpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpc OCA], [https://pdbe.org/2dpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dpc RCSB], [https://www.ebi.ac.uk/pdbsum/2dpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dpc 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=2dpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpc OCA], [https://pdbe.org/2dpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dpc RCSB], [https://www.ebi.ac.uk/pdbsum/2dpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dpc ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ito, T]]		[[Category: Ito T]]
	[[Category: Juan~~, E C.M~~]]		[[Category: Juan ECM]]
	[[Category: Kondo, J]]		[[Category: Kondo J]]
	[[Category: Kurihara, T]]		[[Category: Kurihara T]]
	[[Category: Matsuda, A]]		[[Category: Matsuda A]]
	[[Category: Takenaka, A]]		[[Category: Takenaka A]]
	[[Category: Ueno, Y]]		[[Category: Ueno Y]]
	~~[[Category: B-dna]]~~
	~~[[Category: Dna]]~~
	~~[[Category: Modified nucleotide~~]]

OCA at 10:33, 8 December 2021

2021-12-08T10:33:45Z

← Older revision		Revision as of 10:33, 8 December 2021
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	<StructureSection load='2dpc' size='340' side='right'caption='[[2dpc]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='2dpc' size='340' side='right'caption='[[2dpc]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dpc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DPC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dpc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DPC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMY:(6-AMINOHEXYL)CARBAMIC+ACID'>CMY</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMY:(6-AMINOHEXYL)CARBAMIC+ACID'>CMY</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dp7\|2dp7]], [[2dpb\|2dpb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dp7\|2dp7]], [[2dpb\|2dpb]]</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=2dpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpc OCA], [~~http~~://pdbe.org/2dpc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dpc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dpc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dpc 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=2dpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpc OCA], [https://pdbe.org/2dpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dpc RCSB], [https://www.ebi.ac.uk/pdbsum/2dpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dpc ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:54, 4 March 2020

2020-03-04T07:54:59Z

← Older revision		Revision as of 07:54, 4 March 2020
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	==Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine==		==Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine==
	<StructureSection load='2dpc' size='340' side='right' caption='[[2dpc]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='2dpc' size='340' side='right'caption='[[2dpc]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dpc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DPC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dpc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DPC FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Ito, T]]		[[Category: Ito, T]]
	[[Category: Juan, E C.M]]		[[Category: Juan, E C.M]]

OCA at 06:47, 30 May 2018

2018-05-30T06:47:11Z

← Older revision		Revision as of 06:47, 30 May 2018
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	==Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine==		==Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine==
	<StructureSection load='2dpc' size='340' side='right' caption='[[2dpc]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='2dpc' size='340' side='right' caption='[[2dpc]], [[Resolution\|resolution]] 1.55Å' scene=''>
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	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dp7\|2dp7]], [[2dpb\|2dpb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dp7\|2dp7]], [[2dpb\|2dpb]]</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=2dpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpc OCA], [http://pdbe.org/2dpc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dpc RCSB], [http://www.ebi.ac.uk/pdbsum/2dpc 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=2dpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpc OCA], [http://pdbe.org/2dpc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dpc RCSB], [http://www.ebi.ac.uk/pdbsum/2dpc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dpc ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:48, 10 September 2015

2015-09-10T13:48:12Z

← Older revision		Revision as of 13:48, 10 September 2015
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	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dp7\|2dp7]], [[2dpb\|2dpb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dp7\|2dp7]], [[2dpb\|2dpb]]</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=2dpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dpc RCSB], [http://www.ebi.ac.uk/pdbsum/2dpc 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=2dpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpc OCA], [http://pdbe.org/2dpc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dpc RCSB], [http://www.ebi.ac.uk/pdbsum/2dpc 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 2dpc" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:03, 3 January 2015

2015-01-03T22:03:48Z

← Older revision		Revision as of 22:03, 3 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dpc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DPC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dpc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DPC FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMY:(6-AMINOHEXYL)CARBAMIC+ACID'>CMY</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMY:(6-AMINOHEXYL)CARBAMIC+ACID'>CMY</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dp7\|2dp7]], [[2dpb\|2dpb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dp7\|2dp7]], [[2dpb\|2dpb]]</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=2dpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dpc RCSB], [http://www.ebi.ac.uk/pdbsum/2dpc 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=2dpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dpc RCSB], [http://www.ebi.ac.uk/pdbsum/2dpc 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: Ito, T.]]		[[Category: Ito, T]]
	[[Category: Juan, E C.M.]]		[[Category: Juan, E C.M]]
	[[Category: Kondo, J.]]		[[Category: Kondo, J]]
	[[Category: Kurihara, T.]]		[[Category: Kurihara, T]]
	[[Category: Matsuda, A.]]		[[Category: Matsuda, A]]
	[[Category: Takenaka, A.]]		[[Category: Takenaka, A]]
	[[Category: Ueno, Y.]]		[[Category: Ueno, Y]]
	[[Category: B-dna]]		[[Category: B-dna]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Modified nucleotide]]		[[Category: Modified nucleotide]]

OCA at 07:08, 9 June 2014

2014-06-09T07:08:51Z

← Older revision		Revision as of 07:08, 9 June 2014
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	[[~~Image~~:~~2dpc~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine==
			<StructureSection load='2dpc' size='340' side='right' caption='[[2dpc]], [[Resolution\|resolution]] 1.55Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dpc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DPC FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMY:(6-AMINOHEXYL)CARBAMIC+ACID'>CMY</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
			<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dp7\|2dp7]], [[2dpb\|2dpb]]</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=2dpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dpc RCSB], [http://www.ebi.ac.uk/pdbsum/2dpc PDBsum]</span></td></tr>
			<table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Oligonucleotides containing 5-(N-aminohexyl)carbamoyl-modified uracils have promising features for applications as antigene and antisense therapies. Relative to unmodified DNA, oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine ((N)U) or 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine ((N)U(m)), respectively exhibit increased binding affinity for DNA and RNA, and enhanced nuclease resistance. To understand the structural implications of (N)U and (N)U(m) substitutions, we have determined the X-ray crystal structures of DNA:DNA duplexes containing either (N)U or (N)U(m) and of DNA:RNA hybrid duplexes containing (N)U(m). The aminohexyl chains are fixed in the major groove through hydrogen bonds between the carbamoyl amino groups and the uracil O4 atoms. The terminal ammonium cations on these chains could interact with the phosphate oxygen anions of the residues in the target strands. These interactions partly account for the increased target binding affinity and nuclease resistance. In contrast to (N)U, (N)U(m) decreases DNA binding affinity. This could be explained by the drastic changes in sugar puckering and in the minor groove widths and hydration structures seen in the (N)U(m) containing DNA:DNA duplex structure. The conformation of (N)U(m), however, is compatible with the preferred conformation in DNA:RNA hybrid duplexes. Furthermore, the ability of (N)U(m) to render the duplexes with altered minor grooves may increase nuclease resistance and elicit RNase H activity.

	~~{{STRUCTURE_2dpc\| PDB=2dpc \| SCENE= }}~~		Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules.,Juan EC, Kondo J, Kurihara T, Ito T, Ueno Y, Matsuda A, Takenaka A Nucleic Acids Res. 2007;35(6):1969-77. Epub 2007 Mar 6. PMID:17341465<ref>PMID:17341465</ref>

	~~===Crystal Structure~~ of ~~d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17341465}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2dpc]] is a 2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=2DPC OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:017341465<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Ito, T.]]		[[Category: Ito, T.]]
	[[Category: Juan, E C.M.]]		[[Category: Juan, E C.M.]]

OCA: Protected "2dpc" [edit=sysop:move=sysop]

2012-08-14T16:31:44Z

Protected "2dpc" [edit=sysop:move=sysop]

← Older revision	Revision as of 16:31, 14 August 2012
(No difference)

OCA at 16:31, 14 August 2012

2012-08-14T16:31:41Z

← Older revision		Revision as of 16:31, 14 August 2012
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	~~{{Seed}}~~
	[[Image:2dpc.png\|left\|200px]]		[[Image:2dpc.png\|left\|200px]]

	~~<!--~~
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	{{STRUCTURE_2dpc\| PDB=2dpc \| SCENE= }}		{{STRUCTURE_2dpc\| PDB=2dpc \| SCENE= }}

	===Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine===		===Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17341465}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17341465 is the PubMed ID number.~~
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	{{ABSTRACT_PUBMED_17341465}}		{{ABSTRACT_PUBMED_17341465}}

	==About this Structure==		==About this Structure==
	~~2DPC is a~~ [[~~Single protein~~]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPC OCA].		[[2dpc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPC OCA].

	==Reference==		==Reference==
	Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules., Juan EC, Kondo J, Kurihara T, Ito T, Ueno Y, Matsuda A, Takenaka A, Nucleic Acids Res. 2007;35(6):1969-77. Epub 2007 Mar 6. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17341465 17341465]~~		<ref group="xtra">PMID:017341465</ref><references group="xtra"/>
	~~[[Category: Single protein]]~~
	[[Category: Ito, T.]]		[[Category: Ito, T.]]
	[[Category: Juan, E C.M.]]		[[Category: Juan, E C.M.]]
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	[[Category: Ueno, Y.]]		[[Category: Ueno, Y.]]
	[[Category: B-dna]]		[[Category: B-dna]]
			[[Category: Dna]]
	[[Category: Modified nucleotide]]		[[Category: Modified nucleotide]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 05:15:30 2008''~~

OCA at 02:15, 28 July 2008

2008-07-28T02:15:33Z

← Older revision		Revision as of 02:15, 28 July 2008
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	[[Image:2dpc.~~gif~~\|left\|200px]]		{{Seed}}
			[[Image:2dpc.png\|left\|200px]]

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	{{STRUCTURE_2dpc\| PDB=2dpc \| SCENE= }}		{{STRUCTURE_2dpc\| PDB=2dpc \| SCENE= }}

	~~'''~~Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine~~'''~~		===Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine===


	~~==Overview==~~		<!--
	~~Oligonucleotides containing 5~~-(N-~~aminohexyl)carbamoyl-modified uracils have promising features for applications as antigene and antisense therapies. Relative to unmodified DNA~~, ~~oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine ((N)U) or 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine ((N)U(m))~~, ~~respectively exhibit increased binding affinity for DNA and RNA, and enhanced nuclease resistance. To understand~~ the ~~structural implications of (N)U and (N)U(m) substitutions, we have determined~~ the ~~X-ray crystal structures of DNA:DNA duplexes containing either~~ (~~N)U or (N)U(m) and of DNA~~:RNA hybrid duplexes containing (N)U(m). The aminohexyl chains are fixed in the major groove through hydrogen bonds between the carbamoyl amino groups and the uracil O4 atoms. The terminal ammonium cations on these chains could interact with the phosphate oxygen anions of the residues in the target strands. These interactions partly account for the increased target binding affinity and nuclease resistance. In contrast to (N)U, (N)U(m) decreases DNA binding affinity. This could be explained by the drastic changes in sugar puckering and in the minor groove widths and hydration structures seen in the (N)U(m) containing DNA:DNA duplex structure. ~~The conformation of (N)U(m~~), ~~however,~~ is ~~compatible with the preferred conformation in DNA:RNA hybrid duplexes. Furthermore,~~ the ~~ability of (N)U(m) to render the duplexes with altered minor grooves may increase nuclease resistance and elicit RNase H activity~~.		The line below this paragraph, {{ABSTRACT_PUBMED_17341465}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 17341465 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_17341465}}

	==About this Structure==		==About this Structure==
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	[[Category: B-dna]]		[[Category: B-dna]]
	[[Category: Modified nucleotide]]		[[Category: Modified nucleotide]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 00~~:54:31 2008''
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 05:15:30 2008''