Synthesis and fluorescence properties of dimethylaminonaphthalene–deoxyuridine conjugates as polarity-sensitive probes

The design of probes for monitoring various structures and dynamics of DNA and its surroundings is an important step in understanding biological events accompanying interbiomolecular interaction. We have developed novel fluorescent nucleosides in which the uracil base and the fluorophore are tethered by rigid linkers. They show unique absorption and fluorescence emission spectra. Nucleoside 2 is a fluorophore with high CT character and the fluorescence is very sensitive to solvent polarity. Nucleoside 3 shows absorption and emission maxima with longer wavelength due to extension of the DAN-conjugate system. These fluorophore–deoxyuridine conjugates with unique fluorescence properties would work as reporter probes sensitive to the change in microenvironment around specific sites of DNA.