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

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