4'-C-Methoxy-2'-deoxy-2'-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing

J Am Chem Soc. 2017 Oct 18;139(41):14542-14555. doi: 10.1021/jacs.7b07582. Epub 2017 Oct 6.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Silencing*
  • Nucleic Acid Denaturation
  • Organophosphorus Compounds / chemical synthesis
  • Organophosphorus Compounds / chemistry
  • RNA Interference*
  • RNA Stability*
  • RNA, Small Interfering / chemistry*
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / metabolism*
  • RNAi Therapeutics
  • Ribonucleotides / chemistry*
  • Ribonucleotides / genetics
  • Ribonucleotides / metabolism*
  • Thermodynamics
  • Uridine / chemistry
  • Uridine / metabolism

Substances

  • Organophosphorus Compounds
  • RNA, Small Interfering
  • Ribonucleotides
  • phosphoramidite
  • Uridine

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