Cytosine-specific chemical probing of DNA using bromide and monoperoxysulfate.

Bromination of cytosine and formation of a piperidine-labile site are observed when two simple salts, KBr and KHSO5, are allowed to react with single-stranded oligodeoxynucleotides. Selectivity for C compared with T, G or A is typically a factor of 4 or more; selectivity for Cs in a single-stranded region such as a C-bulge is nearly a factor of 10 compared with duplex Cs. Low reactivity and little base selectivity are observed using duplex DNA, although increased concentrations of reagents lead to complete degradation of the DNA. The results suggest that these conditions for in situ generation of Br2 constitute a useful tool for examination of the exposure of a non-duplex cytosine base in folded DNA structures.