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==X-ray structure of the A-decamer GCGTATACGC with a single 2'-o-butyl thymine in place of T6, Mg-form==
==X-ray structure of the A-decamer GCGTATACGC with a single 2'-o-butyl thymine in place of T6, Mg-form==
<StructureSection load='1wv5' size='340' side='right' caption='[[1wv5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='1wv5' size='340' side='right'caption='[[1wv5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1wv5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WV5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1wv5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WV5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 2.3&#8491;</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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wv6|1wv6]]</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=1wv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv5 OCA], [https://pdbe.org/1wv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wv5 RCSB], [https://www.ebi.ac.uk/pdbsum/1wv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wv5 ProSAT]</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=1wv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wv5 OCA], [http://pdbe.org/1wv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1wv5 PDBsum]</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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1wv5" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Egli, M]]
[[Category: Large Structures]]
[[Category: Inamati, G B]]
[[Category: Egli M]]
[[Category: Lesnik, E A]]
[[Category: Inamati GB]]
[[Category: Manoharam, M]]
[[Category: Lesnik EA]]
[[Category: Minasov, G]]
[[Category: Manoharam M]]
[[Category: Owens, S R]]
[[Category: Minasov G]]
[[Category: Pallan, P S]]
[[Category: Owens SR]]
[[Category: Prakash, T P]]
[[Category: Pallan PS]]
[[Category: Ross, B S]]
[[Category: Prakash TP]]
[[Category: Teplova, M]]
[[Category: Ross BS]]
[[Category: Tereshko, V]]
[[Category: Teplova M]]
[[Category: Dna]]
[[Category: Tereshko V]]

Latest revision as of 16:34, 13 March 2024

X-ray structure of the A-decamer GCGTATACGC with a single 2'-o-butyl thymine in place of T6, Mg-formX-ray structure of the A-decamer GCGTATACGC with a single 2'-o-butyl thymine in place of T6, Mg-form

Structural highlights

1wv5 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1wv5, resolution 2.30Å

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