Improved selectivity for the binding of naphthyridine dimer to guanine–guanine mismatch Original Research Article

Naphthyridine dimer composed of two 2-amino-1,8-naphthyridines and a connecting linker strongly binds to guanine–guanine (G–G) mismatch in duplex DNA. In order to improve G–G selectivity for the binding, we have examined structure modification of the linker. A new naphthyridine dimer possessing 3,6-diazaoctanedioic acid linker binds to G–G mismatch with an association constant of 1.18×107 M−1, which is somewhat weaker than that of the original naphthyridine dimer having a shorter connecting linker. However, the binding of the modified naphthyridine dimer to G–A mismatch was almost negligible as compared to that of the original. This results in a net increase of the selectivity for the binding to G–G mismatch by 4-folds.