CONFORMATION-SPECIFIC DETECTION OF GUANINE IN DNA - ENDS, MISMATCHES, BULGES, AND LOOPS

DNA oxidation promoted by a square-planar complex of nickel(II) (1) in conjunction with KHSO5 provided an excellent method for selectively detecting guanine residues that did not adopt a standard Watson-Crick duplex structure. Sites of modification were indicated by a diagnostic strand scission of DNA induced by subsequent treatment with piperidine. The specificity and, consequently, the utility of this nickel-based reagent were demonstrated through the use of defined oligonucleotide targets. All guanine residues of a random coil reacted readily under the described conditions while the other residues, adenosine, cytidine, and thymidine, remained inert. Most importantly, guanine residues were protected from modification when held within a duplex of complementary paired and stacked bases. This property then allowed for the reliable identification of mispaired, bulged, looped, and terminal guanines from otherwise helical regions of DNA. In addition, the predicted asymmetry of base stacking in a loop structure was confirmed by preferential derivatization of specific guanine residues.