Selective Chemical Labeling of Natural T Modifications in DNA

J Am Chem Soc. 2015 Jul 29;137(29):9270-2. doi: 10.1021/jacs.5b03730. Epub 2015 May 12.

Abstract

We present a chemical method to selectively tag and enrich thymine modifications, 5-formyluracil (5-fU) and 5-hydroxymethyluracil (5-hmU), found naturally in DNA. Inherent reactivity differences have enabled us to tag 5-fU chemoselectively over its C modification counterpart, 5-formylcytosine (5-fC). We rationalized the enhanced reactivity of 5-fU compared to 5-fC via ab initio quantum mechanical calculations. We exploited this chemical tagging reaction to provide proof of concept for the enrichment of 5-fU containing DNA from a pool that contains 5-fC or no modification. We further demonstrate that 5-hmU can be chemically oxidized to 5-fU, providing a strategy for the enrichment of 5-hmU. These methods will enable the mapping of 5-fU and 5-hmU in genomic DNA, to provide insights into their functional role and dynamics in biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA / chemistry*
  • DNA / genetics
  • Models, Molecular
  • Nucleic Acid Conformation
  • Oligodeoxyribonucleotides / chemistry
  • Oligodeoxyribonucleotides / genetics
  • Pentoxyl / analogs & derivatives
  • Pentoxyl / chemistry
  • Thymine / chemistry*
  • Uracil / analogs & derivatives
  • Uracil / chemistry

Substances

  • Oligodeoxyribonucleotides
  • 5-formyluracil
  • 5-hydroxymethyluracil
  • Uracil
  • Pentoxyl
  • DNA
  • Thymine