Naphthalenedicarboxamides as Fluorescent Probes of Inter- and Intramolecular Electron Transfer in Single Strand, Hairpin, and Duplex DNA

Abstract

The 2,6-naphthalenedicarboxamide chromophore has been investigated as a fluorescent probe for DNA hairpin and duplex formation and DNA electron transfer. The high fluorescence quantum yield and long singlet lifetime of this chromophore make it an attractive candidate for these studies. The kinetics of intermolecular quenching of a naphthalenedicarboxamide by nucleosides is dependent upon the nucleoside oxidation potential and solvent. Bis(oligonucleotide) conjugates containing naphthalene linkers have been prepared by means of conventional phosphoramidite chemistry. The base-sequence dependence of the naphthalene fluorescence intensity and decay times in both single-strand and hairpin conjugates indicates that singlet naphthalene is quenched by neighboring dA more efficiently than by dT, in accord with an electron-transfer quenching mechanism. These data are analyzed by means of a three-state model which includes a nonemissive “dark” state. Duplexes formed between complementary naphthalene-linked oligonucleotides display naphthalene excimer emission. The base-sequence dependence of the excimer emission quantum yields indicates that the excimer is not quenched by neighboring dA but that distance-dependent electron-transfer quenching by dG may occur. Quenching serves to protect the naphthalene chromophore from photobleaching in both single strand and duplex structures.