Strong binding of naphthyridine derivatives to a guanine base in DNA duplexes containing an AP site.

By using UV thermal denaturation and isothermal titration calorimetry (ITC), we examine the binding behaviors of a hydrogen bond-forming ligand, 2-acetylamino-7-methyl-1,8-naphthyridine (AcMND), with a guanine base opposite an abasic site (AP site) in a DNA duplex (5'-TCC AGX GCA AC-3'/3'-AGG TCG CGT TG-5', X = AP site, G = target). In the presence of AcMND, the melting temperature (Tm) of the AP site-containing DNA duplex increases by 8.6 degrees C while hardly any change in Tm is observed for a corresponding normal duplex that has no AP sites. The examination by ITC reveals that, in solutions buffered to pH 7.0 (at 10 degrees C, I = 0.11 M), AcMND is able to recognize guanine base with a 1:1 binding constant of 3.4x10(5) M(-1). The ligand-nucleotide interaction is clearly enthalpy driven, with deltaH(o) of -12.5 kcal/mol. We discuss these binding functions of AcMND at the AP site with a view towards development of ligand-based assay for SNPs (single-nucleotide polymorphisms) typing.