Fluorescence properties of quinacrine- and spin-labelled oligodeoxynucleotide

Oligodeoxynucleotides involving a stable nitroxide radical, 5-(2,2,5,5-tetramethyl-3-ethynylpyrroline-1-oxyl)-2-deoxyuridine residue (TMP), and a fluorescence dye, quinacrine (Qu), on each complementary strand and those on the same strand in the duplexes were prepared. Three base-pair units locate between TMP and Qu. The interaction between TMP and the excited singlet Qu has been studied by picosecond transient absorption spectroscopy and fluorometry. From the biphasic fluorescence decay profile, it was suggested that there exist two sites of the dye in the oligodeoxynucleotide with the modifiers in the different complementary strands. In addition, no effective fluorescence quenching was observed for this oigodeoxynucleotide. On the other hand, the triphasic fluorescence decay profile was observed for the oligodeoxynucleotide having Qu and TMP in the same strand and the fluorescence was slightly quenched. Picosecond transient absorption spectroscopy revealed that the enhanced intersystem-crossing by TMP was responsible for the quenching of the fluorescent state of the dye. From these results, it has been concluded that the role of the DNA duplex in the quenching process of the dye by TMP was rather small.