Nucleobase-specific enhancement of Cy3 fluorescence

We report on the role of dye-nucleobase interactions on the photophysical properties of the indocarbocyanine Cy3. The fluorescence efficiency and lifetime of Cy3 increase in the presence of all four nucleoside monophosphates. This behavior correlates with an increase in the activation energy for photoisomerization and a ∼4 nm red shift in the fluorescence spectrum. Changes are more dramatic for the purines (dAMP, dGMP) than the pyrimidines (dCMP, dTMP), and for the nonsulfonated cyanine (DiIC ₂(3)) than the sulfonated dye (Cy3-SE). These results are consistent with a model in which Cy3-nucleoside π-π interactions decrease the efficiency of photoisomerization, increasing the efficiency of fluorescence.