Competitive Binding of Abasic Site-Binding Ligands and Masking Ligands to DNA Duplexes for the Analysis of Single-Base Mutation

Abstract

We describe a competitive binding assay for the analysis of single-base mutation by using abasic site (AP site)-specific binding fluorescent ligands and masking ligands bound to the AP site in DNA duplexes. 2-Amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND) can strongly bind to not only cytosine (C), but also thymine (T) opposite an AP site in the DNA duplexes (K(11)/10(7) M(-1): C, 15; T, 7.0). By contrast, in the presence of lumichrome (Lch) as a masking ligand, ATMND shows a clear binding selectivity for C over T (K(11)/10(7) M(-1): C, 7.0; T, 0.57), which is ascribed to the effective masking effect of Lch to the ATMND-T interaction in the AP site-containing DNA duplexes. It was shown that the competitive binding of ATMND and Lch to the AP site allowed the highly selective detection of C-related single-base mutation in DNAs amplified by polymerase chain reaction.