Analytical Sciences

Ratiometric Fluorescence Detection of Pyrimidine/Purine Transversion by Using a 2-Amino-1,8-naphthyridine Derivative

Hiroyuki SATAKE, Seiichi NISHIZAWA, and Norio TERAMAE

Department of Chemistry, Graduate School of Science, Tohoku University, and CREST, Japan Science and Technology Agency (JST), Aoba-ku, Sendai 980-8578, Japan

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 (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.

J-STAGE: View this article in J-STAGE