Unit

UNIT 4.56 Preparation of Oligodeoxyribonucleotides Containing the Pyrimidine(6–4)pyrimidone Photoproduct by Using a Dinucleotide Building Block

  1. Shigenori Iwai

Published Online: 1 JUN 2013

DOI: 10.1002/0471142700.nc0456s53

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Iwai, S. 2013. Preparation of Oligodeoxyribonucleotides Containing the Pyrimidine(6–4)pyrimidone Photoproduct by Using a Dinucleotide Building Block. Current Protocols in Nucleic Acid Chemistry. 53:4.56:4.56.1–4.56.18.

Author Information

  1. Division of Chemistry, Graduate School of Engineering Science, Osaka University, Osaka, Japan

Publication History

  1. Published Online: 1 JUN 2013

Abstract

This unit describes procedures for the synthesis of a dinucleotide-type building block of the pyrimidine(6–4)pyrimidone photoproduct [(6–4) photoproduct], which is one of the major DNA lesions induced by ultraviolet (UV) light, and its incorporation into oligodeoxyribonucleotides. Although this type of lesion is frequently found at thymine-cytosine sites, the building block of the (6–4) photoproduct formed at thymine-thymine sites can be synthesized much more easily. The problem in the oligonucleotide synthesis is that the (6–4) photoproduct is labile under alkaline conditions. Therefore, building blocks with an amino-protecting group that can be removed by a brief treatment with ammonia water at room temperature must be used for the incorporation of the normal bases. Byproduct formation by the coupling of phosphoramidites with the N3 of the 5′ component should also be considered. This side reaction can be avoided by using benzimidazolium triflate as an activator. Curr. Protoc. Nucleic Acid Chem. 53:4.56.1-4.56.18. © 2013 by John Wiley & Sons, Inc.

Keywords:

  • oligonucleotides;
  • UV damage;
  • DNA repair;
  • xeroderma pigmentosum