2dqp - Revision history

OCA at 18:43, 20 September 2023

OCA — Wed, 20 Sep 2023 18:43:22 GMT

←Older revision		Revision as of 18:43, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dqp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DQP FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dqp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DQP 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>~~</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]] 2.1Å</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=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;~~'>~~[[479d\|479d]], [[2dqo\|2dqo]], [[2dqq\|2dqq]]~~</~~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=2dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqp OCA], [https://pdbe.org/2dqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dqp RCSB], [https://www.ebi.ac.uk/pdbsum/2dqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dqp 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=2dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqp OCA], [https://pdbe.org/2dqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dqp RCSB], [https://www.ebi.ac.uk/pdbsum/2dqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dqp 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: Matsuda, A]]	+	[[Category: Matsuda A]]
-	[[Category: Takenaka, A]]	+	[[Category: Takenaka A]]
-	[[Category: Ueno, Y]]	+	[[Category: Ueno Y]]
-	~~[[Category: A-form rna:dna hybrid duplex]]~~	+
-	~~[[Category: Dna-rna hybrid]]~~	+
-	~~[[Category: Modified nucleotide~~]]	+

OCA at 10:34, 8 December 2021

OCA — Wed, 08 Dec 2021 10:34:31 GMT

←Older revision		Revision as of 10:34, 8 December 2021
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	<StructureSection load='2dqp' size='340' side='right'caption='[[2dqp]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2dqp' size='340' side='right'caption='[[2dqp]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dqp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DQP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dqp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DQP 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></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></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">[[479d\|479d]], [[2dqo\|2dqo]], [[2dqq\|2dqq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[479d\|479d]], [[2dqo\|2dqo]], [[2dqq\|2dqq]]</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=2dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqp OCA], [~~http~~://pdbe.org/2dqp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dqp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dqp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dqp 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=2dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqp OCA], [https://pdbe.org/2dqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dqp RCSB], [https://www.ebi.ac.uk/pdbsum/2dqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dqp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:51, 4 March 2020

OCA — Wed, 04 Mar 2020 07:51:38 GMT

←Older revision		Revision as of 07:51, 4 March 2020
Line 1:		Line 1:

	==Structural analyses of DNA:DNA and RNA:DNA duplexes containing 5-(N-aminohexyl)carbamoyl modified uridines==		==Structural analyses of DNA:DNA and RNA:DNA duplexes containing 5-(N-aminohexyl)carbamoyl modified uridines==
-	<StructureSection load='2dqp' size='340' side='right' caption='[[2dqp]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='2dqp' size='340' side='right'caption='[[2dqp]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dqp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQP FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dqp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQP FirstGlance]. <br>
Line 22:		Line 22:
	__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 06:41, 30 May 2018

OCA — Wed, 30 May 2018 06:41:17 GMT

←Older revision		Revision as of 06:41, 30 May 2018
Line 1:		Line 1:
		+
	==Structural analyses of DNA:DNA and RNA:DNA duplexes containing 5-(N-aminohexyl)carbamoyl modified uridines==		==Structural analyses of DNA:DNA and RNA:DNA duplexes containing 5-(N-aminohexyl)carbamoyl modified uridines==
	<StructureSection load='2dqp' size='340' side='right' caption='[[2dqp]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2dqp' size='340' side='right' caption='[[2dqp]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<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">[[479d\|479d]], [[2dqo\|2dqo]], [[2dqq\|2dqq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[479d\|479d]], [[2dqo\|2dqo]], [[2dqq\|2dqq]]</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=2dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqp OCA], [http://pdbe.org/2dqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dqp RCSB], [http://www.ebi.ac.uk/pdbsum/2dqp 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=2dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqp OCA], [http://pdbe.org/2dqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dqp RCSB], [http://www.ebi.ac.uk/pdbsum/2dqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dqp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 12:23, 11 September 2015

OCA — Fri, 11 Sep 2015 12:23:58 GMT

←Older revision		Revision as of 12:23, 11 September 2015
Line 6:		Line 6:
	<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">[[479d\|479d]], [[2dqo\|2dqo]], [[2dqq\|2dqq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[479d\|479d]], [[2dqo\|2dqo]], [[2dqq\|2dqq]]</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=2dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dqp RCSB], [http://www.ebi.ac.uk/pdbsum/2dqp 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=2dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqp OCA], [http://pdbe.org/2dqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dqp RCSB], [http://www.ebi.ac.uk/pdbsum/2dqp 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 2dqp" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:55, 15 January 2015

OCA — Thu, 15 Jan 2015 16:55:34 GMT

←Older revision		Revision as of 16:55, 15 January 2015
Line 20:		Line 20:
	__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: Matsuda, A.]]	+	[[Category: Matsuda, A]]
-	[[Category: Takenaka, A.]]	+	[[Category: Takenaka, A]]
-	[[Category: Ueno, Y.]]	+	[[Category: Ueno, Y]]
	[[Category: A-form rna:dna hybrid duplex]]		[[Category: A-form rna:dna hybrid duplex]]
	[[Category: Dna-rna hybrid]]		[[Category: Dna-rna hybrid]]
	[[Category: Modified nucleotide]]		[[Category: Modified nucleotide]]

OCA at 15:31, 12 October 2014

OCA — Sun, 12 Oct 2014 15:31:37 GMT

←Older revision		Revision as of 15:31, 12 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2dqp.~~png~~\|~~left~~\|~~200px~~]]	+	==Structural analyses of DNA:DNA and RNA:DNA duplexes containing 5-(N-aminohexyl)carbamoyl modified uridines==
		+	<StructureSection load='2dqp' size='340' side='right' caption='[[2dqp]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2dqp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQP 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></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">[[479d\|479d]], [[2dqo\|2dqo]], [[2dqq\|2dqq]]</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=2dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dqp RCSB], [http://www.ebi.ac.uk/pdbsum/2dqp 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_2dqp\| PDB=2dqp \| 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>

-	~~===Structural analyses~~ of ~~DNA:DNA and RNA:DNA duplexes containing 5-(N-aminohexyl)carbamoyl modified uridines===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17341465}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2dqp]] is a 2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=2DQP 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 "2dqp" [edit=sysop:move=sysop]

OCA — Sun, 06 Jan 2013 11:15:50 GMT

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

←Older revision

Revision as of 11:15, 6 January 2013

OCA at 11:15, 6 January 2013

OCA — Sun, 06 Jan 2013 11:15:46 GMT

←Older revision		Revision as of 11:15, 6 January 2013
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-	{{Seed}}
	[[Image:2dqp.png\|left\|200px]]		[[Image:2dqp.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_2dqp\| PDB=2dqp \| SCENE= }}		{{STRUCTURE_2dqp\| PDB=2dqp \| SCENE= }}

	===Structural analyses of DNA:DNA and RNA:DNA duplexes containing 5-(N-aminohexyl)carbamoyl modified uridines===		===Structural analyses of DNA:DNA and RNA:DNA duplexes containing 5-(N-aminohexyl)carbamoyl modified uridines===

-
-	<!--
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	{{ABSTRACT_PUBMED_17341465}}		{{ABSTRACT_PUBMED_17341465}}

	==About this Structure==		==About this Structure==
-	~~2DQP is a~~ [[~~Protein complex~~]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQP OCA].	+	[[2dqp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQP 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: Protein complex]]~~	+
	[[Category: Ito, T.]]		[[Category: Ito, T.]]
	[[Category: Juan, E C.M.]]		[[Category: Juan, E C.M.]]
Line 32:		Line 19:
	[[Category: Ueno, Y.]]		[[Category: Ueno, Y.]]
	[[Category: A-form rna:dna hybrid duplex]]		[[Category: A-form rna:dna hybrid duplex]]
-	[[Category: Dna/rna ~~complex~~]]	+	[[Category: Dna-rna hybrid]]
	[[Category: Modified nucleotide]]		[[Category: Modified nucleotide]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 05:49:34 2008''

OCA at 02:49, 29 July 2008

OCA — Tue, 29 Jul 2008 02:49:37 GMT

←Older revision		Revision as of 02:49, 29 July 2008
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-	[[Image:2dqp.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2dqp.png\|left\|200px]]

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	{{STRUCTURE_2dqp\| PDB=2dqp \| SCENE= }}		{{STRUCTURE_2dqp\| PDB=2dqp \| SCENE= }}

-	~~'''~~Structural analyses of DNA:DNA and RNA:DNA duplexes containing 5-(N-aminohexyl)carbamoyl modified uridines~~'''~~	+	===Structural analyses of DNA:DNA and RNA:DNA duplexes containing 5-(N-aminohexyl)carbamoyl modified uridines===


-	~~==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: Dna/rna complex]]		[[Category: Dna/rna complex]]
	[[Category: Modified nucleotide]]		[[Category: Modified nucleotide]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 00~~:58:39 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 05:49:34 2008''