Development of new simple molecular probes of DNA bulged structures

NCSi-gb is a neocarzinostatin chromophore (NCS-chrom) metabolite which binds strongly to certain two-base DNA bulges. Compared with previously reported NCSi-gb analogues, a new analogue with a different aminoglycoside position was synthesized, and it showed strong fluorescence and improved binding and sequence selectivity to DNA bulges. The N-dimethylated form of this analogue had a similar binding pattern, and it competitively inhibited bulge-specific cleavage by NCS-chrom.

NCSi-gb is a neocarzinostatin chromophore metabolite which binds strongly to certain two-base DNA bulges. New strongly fluorescent analogues of NCSi-gb possessing aminoglycoside appendage on the two-ring system were synthesized and they resemble NSCi-gb in binding affinity and sequence selectivity for two-base DNA bulges.Figure optionsDownload as PowerPoint slide