Fluorescence-based affinity labeling of nucleobase by hydrogen-bond forming metal complex

A new class of nucleobase-binding fluorescent ligand, ND-DOTA in which 2-amino-5,7-dimethyl-1.8-naphthyridine (ND) is conjugated with 1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid (DOTA) by an amide linker, was synthesized. On the basis of the experimental results obtained from the DNA melting analysis and fluorescent measurement, ND-DOTA-Tb (III) complex was found to strongly recognize cytosine (C) base opposite an abasic site in DNA duplexes. The binding of ND-DOTA-Tb (III) with C was accompanied by significant quenching of the fluorescence from the naphthyridine moiety (lambdamax, 435 nm), while the emission from the Tb based on lanthanoids energy-transfer luminescence (lambdamax, 550 nm) was relatively unaffected. Such a fluorescence response of ND-DOTA-Tb (III) is to be expected to develop the fluorescence-based affinity labelling of a nucleobase at the single-nucleotide segments in DNA duplexes.