Excited-state properties of thymidine and their relevance to its heterogeneous emission in double-stranded DNA

Published results on synthetic polynucleotides point to T as the major emitting fluorophore in DNA. We have reported also that the bases of the nonalternating polynucleotide poly(dA).poly(dT), in which T was selectively excited, undergo large-amplitude motions on the picosecond-nanosecond time scales (S. Georghiou et al., Biophys. J. 70, 1909-1922, 1996). In that study, the fluorescence decay profile of the T bases of this polynucleotide was found to contain a number of components; these may be considered to be the result of the motions of the bases that give rise to a distribution of stacked geometries of varying rigidity as well as dispersion and polar interactions. Here, we report the results of a study that we have undertaken in order to test this hypothesis. To this effect, we have studied the photophysical properties of thymidine (1) in aqueous buffer and in a number of organic solvents and (2) in aqueous sucrose solutions of viscosity extending to 149 cP. The results suggest that the fluorescence quantum yield decreases with an increase in the polarizability of the solvent, whereas it increases with an increase in the solvent polarity (on the basis of the empirical parameter of solvent polarity ETN) or viscosity. These findings suggest the following for the photophysical properties of the T bases in DNA: (1) Base stacking results in two antagonistic effects, namely it causes a reduction in fluorescence as a result of dispersion interactions and an enhancement as a result of a reduction in the motions of the bases and (2) exposure of the bases to the aqueous environment results in fluorescence enhancement.