1wv6 - Revision history

OCA at 13:34, 13 March 2024

OCA — Wed, 13 Mar 2024 13:34:30 GMT

←Older revision		Revision as of 13:34, 13 March 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv6 OCA], [https://pdbe.org/1wv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wv6 RCSB], [https://www.ebi.ac.uk/pdbsum/1wv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wv6 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=1wv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv6 OCA], [https://pdbe.org/1wv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wv6 RCSB], [https://www.ebi.ac.uk/pdbsum/1wv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wv6 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The syntheses of 10 new RNA 2'-O-modifications, their incorporation into oligonucleotides, and an evaluation of their properties such as RNA affinity and nuclease resistance relevant to antisense activity are presented. All modifications combined with the natural phosphate backbone lead to significant gains in terms of the stability of hybridization to RNA relative to the first-generation DNA phosphorothioates (PS-DNA). The nuclease resistance afforded in particular by the 2'-O-modifications carrying a positive charge surpasses that of PS-DNA. However, small electronegative 2'-O-substituents, while enhancing the RNA affinity, do not sufficiently protect against degradation by nucleases. Similarly, oligonucleotides containing 3'-terminal residues modified with the relatively large 2'-O-[2-(benzyloxy)ethyl] substituent are rapidly degraded by exonucleases, proving wrong the assumption that steric bulk will generally improve protection against nuclease digestion. To analyze the factors that contribute to the enhanced RNA affinity and nuclease resistance we determined crystal structures of self-complementary A-form DNA decamer duplexes containing single 2'-O-modified thymidines per strand. Conformational preorganization of substituents, favorable electrostatic interactions between substituent and sugar-phosphate backbone, and a stable water structure in the vicinity of the 2'-O-modification all appear to contribute to the improved RNA affinity. Close association of positively charged substituents and phosphate groups was observed in the structures with modifications that protect most effectively against nucleases. The promising properties exhibited by some of the analyzed 2'-O-modifications may warrant a more detailed evaluation of their potential for in vivo antisense applications. Chemical modification of RNA can also be expected to significantly improve the efficacy of small interfering RNAs (siRNA). Therefore, the 2'-O-modifications introduced here may benefit the development of RNAi therapeutics.
-
-	Probing the influence of stereoelectronic effects on the biophysical properties of oligonucleotides: comprehensive analysis of the RNA affinity, nuclease resistance, and crystal structure of ten 2'-O-ribonucleic acid modifications.,Egli M, Minasov G, Tereshko V, Pallan PS, Teplova M, Inamati GB, Lesnik EA, Owens SR, Ross BS, Prakash TP, Manoharan M Biochemistry. 2005 Jun 28;44(25):9045-57. PMID:15966728<ref>PMID:15966728</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1wv6" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:25, 2 August 2023

OCA — Wed, 02 Aug 2023 11:25:48 GMT

←Older revision		Revision as of 11:25, 2 August 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wv6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WV6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wv6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WV6 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SR:STRONTIUM+ION'>SR</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]] 2.55Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BT:2-O-BUTYL-THYMIDINE'>2BT</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2BT:2-O-BUTYL-THYMIDINE'>2BT</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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;~~'>~~[[1wv5\|1wv5]]~~</~~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=1wv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv6 OCA], [https://pdbe.org/1wv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wv6 RCSB], [https://www.ebi.ac.uk/pdbsum/1wv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wv6 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=1wv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv6 OCA], [https://pdbe.org/1wv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wv6 RCSB], [https://www.ebi.ac.uk/pdbsum/1wv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wv6 ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Egli, M]]	+	[[Category: Egli M]]
-	[[Category: Inamati~~, G B~~]]	+	[[Category: Inamati GB]]
-	[[Category: Lesnik~~, E A~~]]	+	[[Category: Lesnik EA]]
-	[[Category: Manoharam, M]]	+	[[Category: Manoharam M]]
-	[[Category: Minasov, G]]	+	[[Category: Minasov G]]
-	[[Category: Owens~~, S R~~]]	+	[[Category: Owens SR]]
-	[[Category: Pallan~~, P S~~]]	+	[[Category: Pallan PS]]
-	[[Category: Prakash~~, T P~~]]	+	[[Category: Prakash TP]]
-	[[Category: Ross~~, B S~~]]	+	[[Category: Ross BS]]
-	[[Category: Teplova, M]]	+	[[Category: Teplova M]]
-	[[Category: Tereshko, V]]	+	[[Category: Tereshko V]]
-	~~[[Category: Dna~~]]	+

OCA at 16:28, 27 October 2021

OCA — Wed, 27 Oct 2021 16:28:14 GMT

←Older revision		Revision as of 16:28, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1wv6' size='340' side='right'caption='[[1wv6]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='1wv6' size='340' side='right'caption='[[1wv6]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wv6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WV6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WV6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wv6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WV6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BT:2-O-BUTYL-THYMIDINE'>2BT</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BT:2-O-BUTYL-THYMIDINE'>2BT</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wv5\|1wv5]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wv5\|1wv5]]</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=1wv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv6 OCA], [~~http~~://pdbe.org/1wv6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wv6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wv6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wv6 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=1wv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv6 OCA], [https://pdbe.org/1wv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wv6 RCSB], [https://www.ebi.ac.uk/pdbsum/1wv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wv6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 18:05, 22 January 2020

OCA — Wed, 22 Jan 2020 18:05:38 GMT

←Older revision		Revision as of 18:05, 22 January 2020
Line 1:		Line 1:

	==X-ray structure of the A-decamer GCGTATACGC with a single 2'-O-butyl thymine in place of T6, Sr-form==		==X-ray structure of the A-decamer GCGTATACGC with a single 2'-O-butyl thymine in place of T6, Sr-form==
-	<StructureSection load='1wv6' size='340' side='right' caption='[[1wv6]], [[Resolution\|resolution]] 2.55Å' scene=''>	+	<StructureSection load='1wv6' size='340' side='right'caption='[[1wv6]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wv6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WV6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wv6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WV6 FirstGlance]. <br>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Egli, M]]		[[Category: Egli, M]]
	[[Category: Inamati, G B]]		[[Category: Inamati, G B]]

OCA at 16:45, 11 April 2018

OCA — Wed, 11 Apr 2018 16:45:21 GMT

←Older revision		Revision as of 16:45, 11 April 2018
Line 1:		Line 1:
		+
	==X-ray structure of the A-decamer GCGTATACGC with a single 2'-O-butyl thymine in place of T6, Sr-form==		==X-ray structure of the A-decamer GCGTATACGC with a single 2'-O-butyl thymine in place of T6, Sr-form==
	<StructureSection load='1wv6' size='340' side='right' caption='[[1wv6]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='1wv6' size='340' side='right' caption='[[1wv6]], [[Resolution\|resolution]] 2.55Å' 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=2BT:2-O-BUTYL-THYMIDINE'>2BT</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BT:2-O-BUTYL-THYMIDINE'>2BT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wv5\|1wv5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wv5\|1wv5]]</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=1wv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv6 OCA], [http://pdbe.org/1wv6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1wv6 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=1wv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv6 OCA], [http://pdbe.org/1wv6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1wv6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wv6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:32, 11 September 2015

OCA — Fri, 11 Sep 2015 23:32:14 GMT

←Older revision		Revision as of 23:32, 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=2BT:2-O-BUTYL-THYMIDINE'>2BT</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BT:2-O-BUTYL-THYMIDINE'>2BT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wv5\|1wv5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wv5\|1wv5]]</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=1wv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1wv6 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=1wv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv6 OCA], [http://pdbe.org/1wv6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1wv6 PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 16:
	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 1wv6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:52, 22 December 2014

OCA — Mon, 22 Dec 2014 06:52:33 GMT

←Older revision		Revision as of 06:52, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wv6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WV6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wv6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WV6 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BT:2-O-BUTYL-THYMIDINE'>2BT</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BT:2-O-BUTYL-THYMIDINE'>2BT</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wv5\|1wv5]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wv5\|1wv5]]</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=1wv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1wv6 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=1wv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1wv6 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 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Egli, M.]]	+	[[Category: Egli, M]]
-	[[Category: Inamati, G B.]]	+	[[Category: Inamati, G B]]
-	[[Category: Lesnik, E A.]]	+	[[Category: Lesnik, E A]]
-	[[Category: Manoharam, M.]]	+	[[Category: Manoharam, M]]
-	[[Category: Minasov, G.]]	+	[[Category: Minasov, G]]
-	[[Category: Owens, S R.]]	+	[[Category: Owens, S R]]
-	[[Category: Pallan, P S.]]	+	[[Category: Pallan, P S]]
-	[[Category: Prakash, T P.]]	+	[[Category: Prakash, T P]]
-	[[Category: Ross, B S.]]	+	[[Category: Ross, B S]]
-	[[Category: Teplova, M.]]	+	[[Category: Teplova, M]]
-	[[Category: Tereshko, V.]]	+	[[Category: Tereshko, V]]
	[[Category: Dna]]		[[Category: Dna]]

OCA: Protected "1wv6" [edit=sysop:move=sysop]

OCA — Mon, 09 Jun 2014 07:12:05 GMT

Protected "1wv6" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:12, 9 June 2014

OCA at 07:12, 9 June 2014

OCA — Mon, 09 Jun 2014 07:12:04 GMT

←Older revision		Revision as of 07:12, 9 June 2014
Line 1:		Line 1:
-	~~{{Seed}}~~	+	==X-ray structure of the A-decamer GCGTATACGC with a single 2'-O-butyl thymine in place of T6, Sr-form==
-	[[~~Image:~~1wv6.~~png~~\|~~left~~\|~~200px~~]]	+	<StructureSection load='1wv6' size='340' side='right' caption='[[1wv6]], [[Resolution\|resolution]] 2.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1wv6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WV6 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BT:2-O-BUTYL-THYMIDINE'>2BT</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wv5\|1wv5]]</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=1wv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1wv6 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The syntheses of 10 new RNA 2'-O-modifications, their incorporation into oligonucleotides, and an evaluation of their properties such as RNA affinity and nuclease resistance relevant to antisense activity are presented. All modifications combined with the natural phosphate backbone lead to significant gains in terms of the stability of hybridization to RNA relative to the first-generation DNA phosphorothioates (PS-DNA). The nuclease resistance afforded in particular by the 2'-O-modifications carrying a positive charge surpasses that of PS-DNA. However, small electronegative 2'-O-substituents, while enhancing the RNA affinity, do not sufficiently protect against degradation by nucleases. Similarly, oligonucleotides containing 3'-terminal residues modified with the relatively large 2'-O-[2-(benzyloxy)ethyl] substituent are rapidly degraded by exonucleases, proving wrong the assumption that steric bulk will generally improve protection against nuclease digestion. To analyze the factors that contribute to the enhanced RNA affinity and nuclease resistance we determined crystal structures of self-complementary A-form DNA decamer duplexes containing single 2'-O-modified thymidines per strand. Conformational preorganization of substituents, favorable electrostatic interactions between substituent and sugar-phosphate backbone, and a stable water structure in the vicinity of the 2'-O-modification all appear to contribute to the improved RNA affinity. Close association of positively charged substituents and phosphate groups was observed in the structures with modifications that protect most effectively against nucleases. The promising properties exhibited by some of the analyzed 2'-O-modifications may warrant a more detailed evaluation of their potential for in vivo antisense applications. Chemical modification of RNA can also be expected to significantly improve the efficacy of small interfering RNAs (siRNA). Therefore, the 2'-O-modifications introduced here may benefit the development of RNAi therapeutics.

-	<!--	+	Probing the influence of stereoelectronic effects on the biophysical properties of oligonucleotides: comprehensive analysis of the RNA affinity, nuclease resistance, and crystal structure of ten 2'-O-ribonucleic acid modifications.,Egli M, Minasov G, Tereshko V, Pallan PS, Teplova M, Inamati GB, Lesnik EA, Owens SR, Ross BS, Prakash TP, Manoharan M Biochemistry. 2005 Jun 28;44(25):9045-57. PMID:15966728<ref>PMID:15966728</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_1wv6"~~, ~~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_1wv6\| PDB=1wv6 \| SCENE= }}~~	+

-	~~===X-ray structure of the A-decamer GCGTATACGC with~~ a ~~single 2'-O-butyl thymine in place~~ of ~~T6, Sr-form===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_15966728}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 15966728 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_15966728}}~~	+
-		+
-	==~~About this Structure~~==	+
-	~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1WV6 OCA].~~	+
-		+
-	~~==Reference==~~	+
-	Probing the influence of stereoelectronic effects on the biophysical properties of oligonucleotides: comprehensive analysis of the RNA affinity, nuclease resistance, and crystal structure of ten 2'-O-ribonucleic acid modifications., Egli M, Minasov G, Tereshko V, Pallan PS, Teplova M, Inamati GB, Lesnik EA, Owens SR, Ross BS, Prakash TP, Manoharan M, Biochemistry. 2005 Jun 28;44(25):9045-57. PMID:[http:/~~/www.ncbi.nlm.nih.gov/pubmed/15966728 15966728]~~	+
	[[Category: Egli, M.]]		[[Category: Egli, M.]]
	[[Category: Inamati, G B.]]		[[Category: Inamati, G B.]]
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	[[Category: Tereshko, V.]]		[[Category: Tereshko, V.]]
	[[Category: Dna]]		[[Category: Dna]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 13:38:21 2008''

OCA at 10:38, 29 July 2008

OCA — Tue, 29 Jul 2008 10:38:22 GMT

←Older revision		Revision as of 10:38, 29 July 2008
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-	[[Image:1wv6.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1wv6.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1wv6\| PDB=1wv6 \| SCENE= }}		{{STRUCTURE_1wv6\| PDB=1wv6 \| SCENE= }}

-	~~'''~~X-ray structure of the A-decamer GCGTATACGC with a single 2'-O-butyl thymine in place of T6, Sr-form~~'''~~	+	===X-ray structure of the A-decamer GCGTATACGC with a single 2'-O-butyl thymine in place of T6, Sr-form===


-	~~==Overview==~~	+	<!--
-	The ~~syntheses of 10 new RNA 2'-O-modifications~~, ~~their incorporation into oligonucleotides~~, ~~and an evaluation of their properties such as RNA affinity and nuclease resistance relevant to antisense activity are presented. All modifications combined with~~ the ~~natural phosphate backbone lead~~ to ~~significant gains in terms of~~ the ~~stability of hybridization to RNA relative to the first-generation DNA phosphorothioates~~ (~~PS-DNA)~~. ~~The nuclease resistance afforded in particular by the 2'-O-modifications carrying a positive charge surpasses that of PS-DNA~~. However, small electronegative 2'-O-substituents, while enhancing the RNA affinity, do not sufficiently protect against degradation by nucleases. Similarly, oligonucleotides containing 3'-terminal residues modified with the relatively large 2'-O-[2-(benzyloxy)~~ethyl] substituent are rapidly degraded by exonucleases~~, ~~proving wrong~~ the ~~assumption that steric bulk will generally improve protection against nuclease digestion~~. ~~To analyze the factors that contribute to the enhanced RNA affinity and nuclease resistance we determined crystal structures of self~~-~~complementary A~~-form DNA decamer duplexes containing single 2'-O-modified thymidines per strand. Conformational preorganization of substituents, favorable electrostatic interactions between substituent and sugar-phosphate backbone, and a stable water structure in the vicinity of the 2'-O-modification all appear to contribute to the improved RNA affinity. Close association of positively charged substituents and phosphate groups was observed in the structures with modifications that protect most effectively against nucleases. The promising properties exhibited by some of the analyzed 2'-O-modifications may warrant a more detailed evaluation of their potential for in vivo antisense applications. Chemical modification of RNA can also be expected to significantly improve the efficacy of small interfering RNAs (siRNA). Therefore, the 2'-O-modifications introduced here may benefit the development of RNAi therapeutics.	+	The line below this paragraph, {{ABSTRACT_PUBMED_15966728}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 15966728 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_15966728}}

	==About this Structure==		==About this Structure==
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	[[Category: Tereshko, V.]]		[[Category: Tereshko, V.]]
	[[Category: Dna]]		[[Category: Dna]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 14~~:10:50 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 13:38:21 2008''