410d

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==DUPLEX [5'-D(GCGTA+TACGC)]2 WITH INCORPORATED 2'-O-ETHOXYMETHYLENE RIBONUCLEOSIDE==
==DUPLEX [5'-D(GCGTA+TACGC)]2 WITH INCORPORATED 2'-O-ETHOXYMETHYLENE RIBONUCLEOSIDE==
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<StructureSection load='410d' size='340' side='right' caption='[[410d]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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<StructureSection load='410d' size='340' side='right'caption='[[410d]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[410d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=410D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=410D FirstGlance]. <br>
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<table><tr><td colspan='2'>[[410d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=410D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=410D FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene><br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
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<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=T38:2-O-ETHOXYMETHYLENE+THYMIDINE+5-MONOPHOSPHATE'>T38</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=T38:2-O-ETHOXYMETHYLENE+THYMIDINE+5-MONOPHOSPHATE'>T38</scene></td></tr>
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<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=410d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=410d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=410d RCSB], [http://www.ebi.ac.uk/pdbsum/410d PDBsum]</span></td></tr>
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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=410d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=410d OCA], [https://pdbe.org/410d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=410d RCSB], [https://www.ebi.ac.uk/pdbsum/410d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=410d ProSAT]</span></td></tr>
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<table>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Chemically modified nucleic acids are currently being evaluated as potential antisense compounds for therapeutic applications. 2'-O-Ethylene glycol substituted oligoribonucleotides are second-generation antisense inhibitors of gene expression with promising features for in vivo use. Relative to DNA, they display improved RNA affinity and higher nuclease resistance. Moreover, chimeric oligonucleotides with 2'-O-methoxyethyl ribonucleoside wings and a central DNA phosphorothioate window have been shown to effectively reduce the growth of tumors in animal models at low doses. Using X-ray crystallography, we have determined the structures of three A-form DNA duplexes containing the following 2'-O-modified ribothymidine building blocks: 2'-O-methoxyethyl ribo-T, 2'-O-methyl[tri(oxyethyl)] ribo-T, and 2'-O-ethoxymethylene ribo-T. In contrast to 2'-O-ethylene glycol substituents, the presence of a 2'-O-ethoxymethylene group leads to slightly reduced RNA affinity of the corresponding oligonucleotides. The three structures allow a qualitative rationalization of the differing stabilities of duplexes between oligonucleotides comprising these types of 2'-O-modified ribonucleotides and complementary RNAs. The stabilizing 2'-O-ethylene glycol substituents are conformationally preorganized for the duplex state. Thus, the presence of one or several ethylene glycol moieties may reduce the conformational space of the substituents in an oligonucleotide single strand. In addition, most of these preferred conformations appear to be compatible with the minor groove topology in an A-type duplex. Factors that contribute to the conformational rigidity of the 2'-O-substituents are anomeric and gauche effects, electrostatic interactions between backbone and substituent, and bound water molecules.
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Correlating structure and stability of DNA duplexes with incorporated 2'-O-modified RNA analogues.,Tereshko V, Portmann S, Tay EC, Martin P, Natt F, Altmann KH, Egli M Biochemistry. 1998 Jul 28;37(30):10626-34. PMID:9692952<ref>PMID:9692952</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Altmann, K H.]]
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[[Category: Large Structures]]
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[[Category: Egli, M.]]
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[[Category: Altmann KH]]
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[[Category: Martin, P.]]
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[[Category: Egli M]]
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[[Category: Natt, F.]]
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[[Category: Martin P]]
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[[Category: Portmann, S.]]
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[[Category: Natt F]]
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[[Category: Tay, E C.]]
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[[Category: Portmann S]]
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[[Category: Tereshko, V.]]
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[[Category: Tay EC]]
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[[Category: Dna]]
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[[Category: Tereshko V]]

Current revision

DUPLEX [5'-D(GCGTA+TACGC)]2 WITH INCORPORATED 2'-O-ETHOXYMETHYLENE RIBONUCLEOSIDE

PDB ID 410d

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