A pteridine derivative with electron-withdrawing groups for binding and sensing of nucleobases in AP site-containing DNA duplexes

Abstract

A pteridine derivative having electron-withdrawing CF(3) groups, 2-amino-6,7-bis(trifluoromethyl)-4-hydoroxypteridine (2CF(3)-pteridine), is presented as a candidate for multi-functional fluorescent ligand for single-nucleotide polymorphisms (SNPs) typing. In solutions buffered to pH 8.0 (I = 0.1 M, at 5 degrees C), 2CF(3)- pteridine can bind to guanine, cytosine and thymine opposite an abasic site in DNA duplexes (5'-TCTGC GTCCA GXG CAACGCACAC-3'/3'-AGACG CAGGT CNC GTTGCGTGTG-5', X = abasic site; Spacer-C3, N = G, C, A, T). For these three nucleobases, the binding of 2CF(3)-pteridine is explained by 1:1 complexation, and the binding affinities are comparable (K(11) / 10(5) M(-1): G: 3.0; C: 1.6; T: 3.3). Binding-induced fluorescence responses are effectively different between guanine and pyrimidines (C, T): the binding to pyrimidines is accompanied by a significant change in the shape of fluorescence spectra. These binding and sensing properties allow a detection of G/T or G/C mutation based on a single fluorescence ligand.