Detection of small organic analytes by fluorescing molecular switches Original Research Article

A sensor system was developed for the determination of theophylline concentrations based on a theophylline-dependent allosteric ribozyme (Soukup, G. A.; Breaker, R. R. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 3584) in combination with an RNA substrate which is double-labeled with a fluorophore and a quencher dye. In the presence of theophylline, a hammerhead ribozyme domain is switched into an active conformation by the action of a theophylline-binding aptamer domain. Upon substrate cleavage, the quencher is removed from the vicinity of the fluorophore, causing an increased fluorescence signal. Real-time analysis of the cleavage reactions both under single and multiple turnover conditions revealed a dependence on the cleavage rate within a range from 0.01 to 2 mM theophylline. The structurally similar molecule caffeine, however, had no detectable influence on the fluorescence signal.