Sequence-specific DNA strand scission: Evaluation of a methyltransferase-dependent chemoselective ligation

S-adenosyl-L-methionine (SAM) dependent methylation of nucleic acids and proteins is recognized as playing an absolutely vital role in the regulation of gene transcription. In addition to the development of potential chemotherapeutic agents via exploitation of methyltransferases, SAM mimics capable of undergoing transfer to proteins and nucleic acids in an enzyme-dependent fashion hold tremendous promise as biochemical tools by which to dissect and understand biological methylation. Two azido-bearing aziridine-based SAM mimics have been synthesized and are shown to be capable of undergoing methyltransferase-dependent DNA alkylation by M.Taql, M.Hhal, M.EcoRI, and M.Sssl. These azide-modified DNAs undergo efficient Staudinger ligation with functionalized triarylphosphines. Not only does this finding provide a new powerful tool by which to identify unknown methylation sites, but it shows that SAM mimics can be converted into chemical nucleases. It has been established that the site ordinarily methylated can be transformed into a methyltransferase-dependent DNA strand scission agent via attachment of phenanthroline. Upon treatment with copper and a reductant, the DNA conjugates undergo sequence-selective cleavage to reveal regions of DNA methylation.