“Second-generation” fluorogenic RNA-based sensors

•Introduce a type of novel biosensors based on fluorogenic RNA aptamers.•Summarize different design principles of fluorogenic RNA-based sensors.•Discuss about the current applications and challenges of fluorogenic RNAs for cellular imaging and bioanalysis.•Provide several potential pathways to improve the sensitivity, efficiency, and robustness of RNA-based sensors.•Illustrate a guideline and protocol to develop and apply a CHARGE circuit. A fluorogenic aptamer can specifically interact with a fluorophore to activate its fluorescence. These nucleic acid-based fluorogenic modules have been dramatically developed over the past decade, and have been used as versatile reporters in the sensor development and for intracellular imaging. In this review, we summarize the design principles, applications, and challenges of the first-generation fluorogenic RNA-based sensors. Moreover, we discuss some strategies to develop next-generation biosensors with improved sensitivity, selectivity, quantification property, and eukaryotic robustness. Using genetically encoded catalytic hairpin assembly strategy as an example, we further introduce a standard protocol to design, characterize, and apply these fluorogenic RNA-based sensors for in vitro detection and cellular imaging of target biomolecules. By incorporating natural RNA machineries, nucleic acid nanotechnology, and systematic evolution approaches, next-generation fluorogenic RNA-based devices can be potentially engineered to be widely applied in cell biology and biomedicine.