N4 -Allyldeoxycytidine: A New DNA Tag with Chemical Sequencing Power for Pinpointing Labelling Sites, Mapping Epigenetic Markers, and In Situ Imaging.

DNA tagging with base analogues has found numerous applications. To precisely record the DNA labelling information, it would be highly beneficial to develop chemical sequencing tags that can be encoded into DNA as regular bases and decoded as mutant bases following a mild, efficient and bioorthogonal chemical treatment. Here we reported such a DNA tag, N4 -allyldeoxycytidine (a4 dC), for labeling and identifying DNA by in vitro assays. The iodination of a4 dC led to fast and complete formation of 3, N4 -cyclized deoxycytidine, which induced base misincorporation during DNA replication and thus could be located at single base resolution. We explored the applications of a4 dC in pinpointing DNA labelling sites at single base resolution, mapping epigenetic marker N4 -methyldeoxycytidine, and imaging nucleic acids in situ. In addition, mammalian cellular DNA could be metabolically labelled with a4 dC. Our study sheds light on the design of next generation DNA tags with chemical sequencing power.