A new ligand binding to G–G mismatch having improved thermal and alkaline stability

Naphthyridine dimer (ND) specially binds to guanine–guanine (G–G) mismatch in duplex DNA. In order to improve the thermal and alkaline stability and binding ability of the ligand, we have examined structural modification of the linker. A new ligand (NNC) possessing 2-amino-1,8-naphthyridines and a carbamate linker is much more thermally stable than ND. The half-life of NNC is 2.5 times longer than that of ND at 80 °C. NNC is also much more stable than ND under alkaline conditions. In addition, NNC binds to G–G mismatch more strongly than ND. The improved stability and the binding of NNC to the G–G mismatch would be suitable for the practical use of NNC-immobilized sensor.