In combination with abasic site (AP site)-containing
oligodeoxynucleotides (ODNs), we demonstrate potential use of a hydrogen bond forming
ligand,
2-amino-7-methyl-1,8-naphthyridine (AMND), for the fluorescence detection of the
cytosine (C)/
guanine (G) mutation sequence of the
cancer repression gene p53. Our method is based on construction of the AP site in ODN duplexes, which allows small synthetic
ligands to bind to target nucleobases accompanied by fluorescence signaling: an AP site-containing ODN is hybridized with a target ODN so as to place the AP site toward a target nucleobase, by which hydrophobic microenvironments are provided for
ligands to recognize target nucleobases through hydrogen-bonding. In 10mM
sodium cacodylate buffer solutions (pH, 7.0) containing 100mM NaCl and 1.0mM
EDTA, AMND is found to strongly bind to C (K(d)=1.5x10(-6)M) in the target ODN while the binding affinity for G is relatively moderate (K(d)=50x10(-6)M). Significant fluorescence quenching of AMND is observed only when binding to C, making it possible to judge the C/G transversion with the naked eye.