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Dimeric naphthyridine was designed and synthesized as a novel ligand that specifically binds to G-G mismatch, one of four SNP types. In the presence of dimeric naphthyridine, CD spectra of the G-G mismatch containing duplex noticeably changed, being accompanied by the induced CD at 300-350 nm, whereas no CD spectral change was observed for normal duplex. DNaseI footprinting titration indicated a selective binding of dimeric naphthyridine to the G-G mismatch with a dissociation constant of 53 nM.

New method for scanning of single-nucleotide polymorphisms (SNPs): Recognition of guanine-guanine mismatches by dimeric naphthyridine