title: Selective Chemical Labeling of Natural T Modifications in DNA.
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.
authors.affiliation: †Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
authors.forename: Robyn E
authors.initials: RE
authors.lastname: Hardisty
authors.affiliation: †Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
authors.forename: Fumiko
authors.initials: F
authors.lastname: Kawasaki
authors.affiliation: †Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
authors.forename: Aleksandr B
authors.initials: AB
authors.lastname: Sahakyan
authors.affiliation: †Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.|‡Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.|§School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, U.K.
authors.forename: Shankar
authors.initials: S
authors.lastname: Balasubramanian
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000235:genetics; D010432:Pentoxyl / Q000031:analogs & derivatives / Q000737:chemistry; D013941:Thymine / Q000737:chemistry*; D014498:Uracil / Q000031:analogs & derivatives / Q000737:chemistry
chemical_list: D009838:Oligodeoxyribonucleotides; C007777:5-formyluracil; C008055:5-hydroxymethyluracil; D014498:Uracil; D010432:Pentoxyl; D004247:DNA; D013941:Thymine