Unit

UNIT 4.21 Uridine 2′-Carbamates: Facile Tools for Oligonucleotide 2′-Functionalization

  1. Vladimir A. Korshun1,
  2. Dmitry A. Stetsenko2,
  3. Michael J. Gait2

Published Online: 1 FEB 2004

DOI: 10.1002/0471142700.nc0421s15

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Korshun, V. A., Stetsenko, D. A. and Gait, M. J. 2004. Uridine 2′-Carbamates: Facile Tools for Oligonucleotide 2′-Functionalization. Current Protocols in Nucleic Acid Chemistry. 15:4.21:4.21.1–4.21.26.

Author Information

  1. 1

    Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia

  2. 2

    Medical Research Council, Laboratory of Molecular Biology, Cambridge, United Kingdom

Publication History

  1. Published Online: 1 FEB 2004
  2. Published Print: DEC 2003

Abstract

A facile method for preparation of uridine 2′-carbamate derivatives based on reaction of 3′,5′-disilyl-protected uridine with 1,1′-carbonyldiimidazole followed by treatment with an aliphatic amine is presented. A phosphoramidite monomer suitable for automated oligonucleotide synthesis is obtained in a few steps. The compounds are useful for the introduction of various labels and modifications into an oligonucleotide chain. Although 2′-carbamate modification is somewhat destabilizing for DNA-DNA and DNA-RNA duplexes, it is suitable for the direction of ligands into the minor groove of duplexes or at non-base-paired sites (e.g., loops and bulges) of oligonucleotides. Pyrene-modified oligonucleotide 2′-carbamates show a considerable increase in fluorescence intensity upon hybridization to a complementary RNA (but not DNA).

Keywords:

  • nucleoside;
  • uridine carbamate;
  • oligonucleotide modification;
  • duplex stability;
  • pyrene;
  • fluorescence