Unit

UNIT 4.47 Preparation of DNA Containing 5-Hydroxymethyl-2′-Deoxycytidine Modification Through Phosphoramidites with TBDMS as 5-Hydroxymethyl Protecting Group

  1. Qing Dai,
  2. Chuan He

Published Online: 1 DEC 2011

DOI: 10.1002/0471142700.nc0447s47

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Dai, Q. and He, C. 2011. Preparation of DNA Containing 5-Hydroxymethyl-2′-Deoxycytidine Modification Through Phosphoramidites with TBDMS as 5-Hydroxymethyl Protecting Group. Current Protocols in Nucleic Acid Chemistry. 47:4.47:4.47.1–4.47.18.

Author Information

  1. Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois

Publication History

  1. Published Online: 1 DEC 2011
  2. Published Print: DEC 2011

Abstract

This unit describes procedures for preparation of two phosphoramidite building blocks III and IV, both containing a TBDMS as 5-CH2OH-protecting group. Phosphoramidites III and IV allow efficient incorporation of 5-hmC into DNA and a “one-step” deprotection procedure to cleanly remove all the protecting groups. A “two-step” deprotection strategy is compatible with ultramild DNA synthesis, which enables the synthesis of 5hmC-containing DNA with additional modifications. Methods are also presented for their incorporation into oligonucleotides by solid-phase synthesis, subsequent deprotection, and HPLC analysis. Curr. Protoc. Nucleic Acid Chem. 47:4.47.1-4.47.18. © 2011 by John Wiley & Sons, Inc.

Keywords:

  • 5-Hydroxymethylcytosine;
  • DNA modification;
  • oligodeoxyribonucleotide (ODN);
  • phosphoramidite;
  • solid-phase synthesis;
  • genomic DNA;
  • epigenetic;
  • ultramild deprotection