Synthesis of 5-Cyanomethyluridine (cnm5 U) and 5-Cyanouridine (cn5 U) Phosphoramidites and Their Incorporation into RNA Oligonucleotides

Curr Protoc Nucleic Acid Chem. 2020 Sep;82(1):e114. doi: 10.1002/cpnc.114.

Abstract

This article contains detailed synthetic protocols for preparation of 5-cyanomethyluridine (cnm5 U) and 5-cyanouridine (cn5 U) phosphoramidites. The synthesis of the cnm5 U phosphoramidite building block starts with commercially available 5-methyluridine (m5 C), followed by bromination of the 5-methyl group to install the cyano moiety using TMSCN/TBAF. The cn5 U phosphoramidite is obtained by regular Vorbrüggen glycosylation of the protected ribofuranose with silylated 5-cyanouracil. These two modified phosphoramidites are suitable for synthesis of RNA oligonucleotides on solid phase using conventional amidite chemistry. Our protocol provides access to two novel building blocks for constructing RNA-based therapeutics. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Preparation of cnm5 U and cn5 U phosphoramidites Basic Protocol 2: Synthesis, purification, and characterization of cnm5 U- and cn5 U-modified RNA oligonucleotides.

Keywords: cyano-modification; nucleic acids; phosphoramidite; solid phase synthesis.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chromatography, Thin Layer
  • Cyanides / chemistry*
  • Oligoribonucleotides / chemical synthesis
  • Oligoribonucleotides / chemistry*
  • Oligoribonucleotides / isolation & purification
  • Organophosphorus Compounds / chemical synthesis*
  • Organophosphorus Compounds / chemistry
  • Proton Magnetic Resonance Spectroscopy
  • Solid-Phase Synthesis Techniques / methods
  • Spectrometry, Mass, Electrospray Ionization

Substances

  • Cyanides
  • Oligoribonucleotides
  • Organophosphorus Compounds
  • phosphoramidite