View source for 6vem


==Structure of RNA octamer==
<StructureSection load='6vem' size='340' side='right'caption='[[6vem]], [[Resolution|resolution]] 1.56&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VEM FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.56&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GMX:2-amino-9-(6-deoxy-5-O-phosphono-beta-D-allofuranosyl)-3,9-dihydro-6H-purin-6-one'>GMX</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></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=6vem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vem OCA], [https://pdbe.org/6vem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vem RCSB], [https://www.ebi.ac.uk/pdbsum/6vem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vem ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Various chemical modifications have been identified that enhance potency of small interfering RNAs (siRNAs) and that reduce off-target effects, immune stimulation, and toxicities of metabolites of these therapeutic agents. We previously described 5'-C-methyl pyrimidine nucleotides also modified at the 2' position of the sugar. Here, we describe the synthesis of 2'-position unmodified 5'-(R)- and 5'-(S)-C-methyl guanosine and evaluation of these nucleotides in the context of siRNA. The (R) isomer provided protection from 5' exonuclease and the (S) isomer provided protection from 3' exonuclease in the context of a terminally modified oligonucleotide. siRNA potency was maintained when these modifications were incorporated at the tested positions of sense and antisense strands. Moreover, the corresponding 5' triphosphates were not substrates for mitochondrial DNA polymerase. Models generated based on crystal structures of 5' and 3' exonuclease oligonucleotide complexes with 5'-(R)- and 5'-(S)-C-methyl substituents attached to the 5'- and 3'-terminal nucleotides, respectively, provided insight into the origins of the observed protections. Structural properties of 5'-(R)-C-methyl guanosine incorporated into an RNA octamer were analysed by X-ray crystallography, and the structure explains the loss in duplex thermal stability for the (R) isomer compared with the (S) isomer. Finally, the effect of 5'-C-methylation on endoribonuclease activity has been explained.

Synthesis, chirality-dependent conformational and biological properties of siRNAs containing 5'-(R)- and 5'-(S)-C-methyl-guanosine.,Mikami A, Erande N, Matsuda S, Kel'in A, Woods LB, Chickering T, Pallan PS, Schlegel MK, Zlatev I, Egli M, Manoharan M Nucleic Acids Res. 2020 Oct 9;48(18):10101-10124. doi: 10.1093/nar/gkaa750. PMID:32990754<ref>PMID:32990754</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6vem" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Egli M]]
[[Category: Pallan PS]]