Binding analysis between naphthyridine dimers and GG mismatch DNA

Kinetics and thermodynamics studies of the binding between naphthyridine dimer and DNA duplexes having a G-G mismatch sequence were performed by using Surface Plasmon Resonance (SPR) assay. Naphthyridine dimers possessing a different length of PEG linker were synthesized and immobilized to the dextran surface of the sensor chip to obtain an improved sensitivity of the SPR sensor toward a G-G mismatch. The effect of the directly neighboring base pair to the G-G mismatch was estimated from the thermodynamic parameters of the complex. These results indicate that stacking with adjacent base pair and naphthyridine dimer is the key roll for the formation of the complex between mismatched base pair and naphthyridine dimer.