Dimeric 2-amino-1, 8-naphthyridine selectively binds to a GG mismatch with high affinity (K d= 53 nM). We have investigated a binding mechanism of naphthyridine dimer 2 to a GG mismatch by spectroscopic studies, thermodynamic analysis, and structure-activity studies for the thermal stabilization of the mismatch. 1H NMR spectra of a complex of 2 with 9-mer duplex d (CATCGGATG) 2 containing a GG mismatch showed that all hydrogens in two ...