Unit

UNIT 3.9 3-(N-tert-Butylcarboxamido)-1-propyl and 4-Oxopentyl Groups for Phosphate/Thiophosphate Protection in Oligodeoxyribonucleotide Synthesis

  1. Andrzej Wilk1,
  2. Marcin K. Chmielewski1,
  3. Andrzej Grajkowski1,
  4. Serge L. Beaucage1,
  5. Lawrence R. Phillips2

Published Online: 1 FEB 2003

DOI: 10.1002/0471142700.nc0309s11

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Wilk, A., Chmielewski, M. K., Grajkowski, A., Beaucage, S. L. and Phillips, L. R. 2003. 3-(N-tert-Butylcarboxamido)-1-propyl and 4-Oxopentyl Groups for Phosphate/Thiophosphate Protection in Oligodeoxyribonucleotide Synthesis. Current Protocols in Nucleic Acid Chemistry. 11:3.9:3.9.1–3.9.16.

Author Information

  1. 1

    Food and Drug Administration, Bethesda, Maryland

  2. 2

    National Cancer Institute, Frederick, Maryland

Publication History

  1. Published Online: 1 FEB 2003
  2. Published Print: DEC 2002

Abstract

This unit provides procedures for the preparation of deoxyribonucleoside phosphoramidites and appropriate phosphordiamidite precursors with P(III) protecting groups different than the standard 2-cyanoethyl group. Specifically, these phosphoramidites are functionalized with the 3-(N-tert-butylcarboxamido)-1-propyl or 4-oxopentyl groups. The usefulness of these novel deoxyribonucleoside phosphoramidites in the solid-phase synthesis of a 20-mer DNA oligonucleotide and its phosphorothioated analog is demonstrated. It is also shown that removal of the 3-(N-tert-butylcarboxamido)-1-propyl phosphate/thiophosphate-protecting group from these oligonucleotides is rapidly effected under thermolytic conditions at neutral pH, whereas the 4-oxopentyl group is preferably removed by treatment with pressurized ammonia gas or concentrated ammonium hydroxide at ambient temperature. These detailed methods constitute an economical and alkylation-free approach to large-scale preparations of therapeutic oligonucleotides.