UNIT 3.12 Nucleoside Phosphoramidites Containing Cleavable Linkers

  1. Richard T. Pon

Published Online: 1 JAN 2006

DOI: 10.1002/0471142700.nc0312s23

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Pon, R. T. 2006. Nucleoside Phosphoramidites Containing Cleavable Linkers. Current Protocols in Nucleic Acid Chemistry. 23:3.12:3.12.1–3.12.24.

Author Information

  1. University of Calgary, Calgary, Alberta, Canada

Publication History

  1. Published Online: 1 JAN 2006
  2. Published Print: DEC 2005


Phosphoramidite reagents (linker phosphoramidites) containing a cleavable 3′-ester linkage between the nucleoside and the phosphoramidite group can be used to attach the first nucleoside to a solid-phase support. Inexpensive underivatized supports such as LCAA-CPG can then be used as universal supports for oligonucleotide synthesis. No modifications to synthesis coupling conditions and no 3′-dephosphorylation are required. Only oligonucleotides with terminal 3′-OH ends are produced. Phosphoramidites containing both a succinate and a sulfonyldiethanol linkage are particularly useful and create oligonucleotides with both a 3′-OH and 5′-phosphate. In addition, by using these reagents, one oligonucleotide sequence can be added onto the 5′-end of another (tandem synthesis) to produce a string of multiple oligonucleotides linked end-to-end. Deprotection releases the oligonucleotides from each other to yield a mixture of oligonucleotides. This approach is particularly useful for making pairs of PCR primers or both strands of a double-stranded sequence in a single operation.


  • linker phosphoramidites;
  • solid-phase supports;
  • tandem oligonucleotide synthesis;
  • 96-well plate synthesis;
  • high-throughput synthesis;
  • support derivatization