Uridine 2'-carbamates: facile tools for oligonucleotide 2'-functionalization

Curr Protoc Nucleic Acid Chem. 2004 Feb:Chapter 4:Unit 4.21. doi: 10.1002/0471142700.nc0421s15.

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).

Publication types

  • Review

MeSH terms

  • Acylation
  • Base Sequence
  • Carbamates / chemical synthesis*
  • Carbamates / chemistry*
  • Carbamates / pharmacology
  • Models, Biological
  • Oligonucleotides / analysis
  • Oligonucleotides / chemistry*
  • Oligonucleotides / isolation & purification
  • Oligonucleotides / pharmacology*
  • Organophosphorus Compounds / chemical synthesis
  • Uridine / chemical synthesis
  • Uridine / chemistry*

Substances

  • Carbamates
  • Oligonucleotides
  • Organophosphorus Compounds
  • phosphoramidite
  • Uridine