Volume 22 (2006) Issue 2 Pages 195-197
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/M-1: T, 8.1 × 106; C, 2.5 × 106; G, 0.33 × 106; A, 0.27 × 106). The binding of Naph-NBD is accompanied by significant quenching of the fluorescence from the naphthyridine moiety (λmax, 409 nm), while the emission from the NBD (λmax, 544 nm) is relatively unaffected. Such a fluorescence response of Naph-NBD allows the emission ratio detection of pyrimidine/purine transversion.