A novel naphthyridine tetramer that recognizes tandem G-G mismatches by the formation of an interhelical complex

We have designed and synthesized a novel naphthyridine tetramer, p-NCTB, for the recognition of tandem guanine-guanine (G-G) mismatches in DNA. p-NCTB possesses a p-biphenyl linker connecting two naphthyridine carbamate dimer (NCD) moieties that recognize G-G mismatches. p-NCTB preferentially bound to tandem G-G mismatches in dCGGG/dCGGG over dCGG/dCGG. Two dCGGG/dCGGG sites were simultaneously recognized and were noncovalently cross-linked via the formation of inter- and intrastrand complexes with p-NCTB. The intrastrand binding was more favorable, which could allow p-NCTB to bind selectively to a sequence containing multiple dCGGG/dCGGG sites.