UNIT 1.1 Palladium-Mediated C5 Substitution of Pyrimidine Nucleosides

  1. Mohammad Ahmadian1,
  2. Douglas A. Klewer2,
  3. Donald E. Bergstrom3

Published Online: 1 MAY 2001

DOI: 10.1002/0471142700.nc0101s00

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Ahmadian, M., Klewer, D. A. and Bergstrom, D. E. 2001. Palladium-Mediated C5 Substitution of Pyrimidine Nucleosides. Current Protocols in Nucleic Acid Chemistry. 00:1.1:1.1.1–1.1.18.

Author Information

  1. 1

    Cerus Corp., Concord, California

  2. 2

    Texas A&M University, College Station, Texas

  3. 3

    Purdue University, West Lafayette, Indiana

Publication History

  1. Published Online: 1 MAY 2001
  2. Published Print: FEB 2000


One of the most efficient ways to link a reporter group to oligonucleotides is through the incorporation of a modified nucleoside during automated oligonucleotide synthesis. To be useful, it is important that the reporter group not interfere in hybridization reactions. This unit describes two linkers that can be used for the incorporation of a reporter group at the C5 position of deoxyuridine: a flexible aminoethylthioether linker, and a rigid amidopropynyl linker. The latter is suffciently long and positioned so that the reporter group lies outside the major groove of the DNA duplex.