Stacking interactions in fluorescent nucleotide analogs containing 1-aminonaphthalene-5-sulfonate at the phosphoryl...

The conformational properties of nucleotides containing the fluorophore 1-aminonaphthalene-5-sulfonate attached via a gamma-phosphoamidate bond have been examined. Measurements of fluorescence excitation spectra show that energy absorbed by adenine in the ATP analog is transferred to the naphthalene moiety with an efficiency of approximately 43%. In nonpolar solvents transfer is almost eliminated. The fluorescence intensity of the UTP analog is quenched. Measurements of quantum yield and excited state lifetime show that this occurs by both dynamic and static mechanisms. Thus, fluorescence studies show that both the purine and pyrimidine analogs exist in an equilibrium mixture of stacked and unstacked forms. NMR studies show that the base and ribose protons of the ATP and UTP analogs are shifted upfield by about 0.2 to 0.3 ppm, presumably due to ring current effects produced by stacking interactions. Phosphorus NMR spectra of the ATP analog are generally similar to spectra of unmodified ATP. The strong dependence on conformation of the fluorescence of the pyrimidine analogs may prove useful in studies of protein-nucleotide interactions.