Fluorescent Ribozyme and Deoxyribozyme Sensors

The development of allosteric nucleic acid enzymes (NAEs) has made NAEs very attractive for a wide variety of biotechnological applications, including biosensing, diagnostics, drug screening, and molecular computation. Although NAEs alone might have limited values for analytical application due to the rather small scope of their substrates and cofactors, modular characteristics of aptamers and NAEs permit the easy design of combined sensors where the aptamer acts as the molecular recognition element (MRE) and the NAE functions as a reporter. To facilitate the exploitation of NAEs for biosensing applications, fluorescence methods have been increasingly explored as better alternatives to radioisotope-based detection techniques. In this chapter, we first survey the strategies that have been employed to graft fluorescence-signaling moieties onto NAEs. We then review our experimental efforts in creating a group of fluorescence-signaling and RNA-cleaving deoxyribozymes (DNAzymes) intended for the design of fluorescent sensors. Last, we discuss the diverse engineering approaches that can transmit the binding status of an aptamer to the activation or repression of catalytic activity in fluorescent NAE sensors.