5VR4 image
Entry Detail
PDB ID:
5VR4
Keywords:
Title:
RNA octamer containing 2'-F-4'-OMe U.
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2017-05-10
Release Date:
2017-10-04
Method Details:
Experimental Method:
Resolution:
1.50 Å
R-Value Free:
0.24
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 43 21 2
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:RNA (5'-R(*CP*GP*AP*AP*(UMO)P*UP*CP*G)-3')
Chain IDs:A, B, C, D
Chain Length:8
Number of Molecules:4
Biological Source:synthetic construct
Ligand Molecules
Primary Citation
4'-C-Methoxy-2'-deoxy-2'-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing.
J. Am. Chem. Soc. 139 14542 14555 (2017)
PMID: 28937776 DOI: 10.1021/jacs.7b07582

Abstact

We designed novel 4'-modified 2'-deoxy-2'-fluorouridine (2'-F U) analogues with the aim to improve nuclease resistance and potency of therapeutic siRNAs by introducing 4'-C-methoxy (4'-OMe) as the alpha (C4'α) or beta (C4'β) epimers. The C4'α epimer was synthesized by a stereoselective route in six steps; however, both α and β epimers could be obtained by a nonstereoselective approach starting from 2'-F U. 1H NMR analysis and computational investigation of the α-epimer revealed that the 4'-OMe imparts a conformational bias toward the North-East sugar pucker, due to intramolecular hydrogen bonding and hyperconjugation effects. The α-epimer generally conceded similar thermal stability as unmodified nucleotides, whereas the β-epimer led to significant destabilization. Both 4'-OMe epimers conferred increased nuclease resistance, which can be explained by the close proximity between 4'-OMe substituent and the vicinal 5'- and 3'-phosphate group, as seen in the X-ray crystal structure of modified RNA. siRNAs containing several C4'α-epimer monomers in the sense or antisense strands triggered RNAi-mediated gene silencing with efficiencies comparable to that of 2'-F U.

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