Hydrogen bond-mediated binding of ligands to a nucleobase at a gap site in a DNA duplex and its use for fluorescence detection of single-nucleotide polymorphisms.

Here we report on the strong and selective binding of a hydrogen bond-forming ligand, 2-amino-7-methyl-1,8-naphthyridine (AMND), to a nucleobase at a gap site in DNA duplexes. In solutions buffered to pH 7.0 (at 20 degrees C, I = 0.11 M), AMND is found to selectively recognize cytosine (C) base over other nucleotides, and the 1:1 association constant reaches 3.2x10(5) M(-1) when binding to C. The ligand-nucleotide interaction results in significant fluorescence quenching of AMND, which is highly selective to C. These sensing functions of AMND at the gap site are utilized for the development of ligand-based fluorescence assay for SNPs (single-nucleotide polymorphisms) typing.