Ratiometric fluorescence detection of pyrimidine/purine transversion by using a 2-amino-1,8-naphthyridine derivative

A new class of abasic site-binding fluorescence ligands, Naph-NBD in which 7-nitrobenzo-2-oxa-1,3-diazole (NBD) is connected to 2-amino-7-methyl-1,8- naphthyridine (Naph) by a propylene linker, is presented for the ratiometric assay for SNPs typing. In solutions buffered to pH 7.0 (I = 0.11 M, at 5°C), Naph-NBD is found to selectively recognize pyrimidine bases over purine bases opposite the abasic site in DNA duplexes (K₁₁/M¹: T, 8.1 x 10⁶; C, 2.5 x 10⁶; G, 0.33 x 10⁶; A, 0.27 x 10⁶). The binding of Naph-NBD is accompanied by significant quenching of the fluorescence from the naphthyridine moiety (λ_max;, 409 nm), while the emission from the NBD (λ_max;, 544 nm) is relatively unaffected. Such a fluorescence response of Naph-NBD allows the emission ratio detection of pyrimidine/purine transversion. 2006