Unit

UNIT 4.53 Synthesis of Oligodeoxynucleotides with 5′-Caps Binding RNA Targets

  1. Simone Egetenmeyer,
  2. Clemens Richert

Published Online: 1 DEC 2012

DOI: 10.1002/0471142700.nc0453s51

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Egetenmeyer, S. and Richert, C. 2012. Synthesis of Oligodeoxynucleotides with 5′-Caps Binding RNA Targets. Current Protocols in Nucleic Acid Chemistry. 51:4.53:4.53.1–4.53.21.

Author Information

  1. Institute for Organic Chemistry, University of Stuttgart, Stuttgart, Germany

Publication History

  1. Published Online: 1 DEC 2012

Abstract

Protocols for the synthesis of oligodeoxynucleotides with a short peptidyl substituent linked to the 5′-O-terminus through a phosphodiester bond are presented. The example given is a peptidyl cap consisting of the residues of l-prolinol, glycine, and the acyl residue of oxolinic acid. DNA probes with this cap, also known as ogOA cap, give melting point increases for duplexes with RNA targets and improve mismatch discrimination at the terminus. The cap is either introduced in one step, using a newly developed phosphoramidite reagent, or assembled on the DNA chain. The step-wise assembly of the peptidyl chain is advantageous for combinatorial studies aimed at the optimization of a cap structure. The block coupling method, introducing the preassembled cap in one step, is attractive for routine use of a cap already optimized for a given application. Cap-bearing probes can increase fidelity of hybridization in a genomic context. They can be synthesized by automated DNA synthesis. Curr. Protoc. Nucleic Acid Chem. 51:4.53.1-4.53.21. © 2012 by John Wiley & Sons, Inc.

Keywords:

  • oligonucleotides;
  • phosphoramidite;
  • peptides;
  • controlled pore glass;
  • hybridization probes