Characterization of two adenosine analogs as fluorescence probes in RNA

The fluorescence properties of two adenosine analogs, 2-(3-phenylpropyl)adenosine [A-3CPh] and 2-(4-phenylbutyl)adenosine [A-4CPh], are reported. As monomers, the quantum yields and the mean lifetimes are 0.011 and 6.22 ns for A-3CPh and 0.007 and 7.13 ns for A-4CPh, respectively. Surprisingly, the quantum yields of the two probes are enhanced 11- to 82-fold upon incorporation into RNA, while the mean lifetimes decrease 23–40%. The data suggest that a subpopulation of molecules is responsible for the fluorescence characteristics and that the distribution of emitting and non-emitting structures is altered upon incorporation of the probes into RNA. Thus, although both adenosine analogs have low quantum yields as monomers, their fluorescence signals are significantly enhanced in RNA. Thermodenaturation experiments and CD spectroscopy indicate that incorporation of the adenosine analogs into three different RNAs does not alter their global structure or stability. Therefore, these probes should be useful for probing events occurring close to the site of modification.