Benchmarking RNA Switches for Diagnostic Applications

The current golden standards employed for pathogen detection are generally too expensive and/or require technical expertise that becomes prohibitive for their widespread use in developing nations. Recent developments in RNA design and engineering have led to an explosion in the potential of this biomolecule for the constructing of sophisticated sensors and bio-circuitry aimed at a plethora of problem solving applications. Centrally to this idea is the plethora of natural, and more importantly, laboratory designed RNA regulatory switches. Upon the binding of nucleic acid or small ligands, these switches can be tailored to act upon both the transcriptional and translational landscape. We are currently working to characterize and further improve upon RNA-based bio-circuitry in order to ascertain what is needed to convert input signals, such as pathogen DNA/RNA, into rapid and comprehensible visual outputs. Specifically we will present work on the characterization of several reported RNA switches. Using fluorescent and colorimetric outputs, we have begun to establish a benchmark characterization to compare the performance of switches in terms of speed of response, dynamic range and limit of detection. This also enables us to explore additional important factors such as constraints for naked eye visualization. In harnessing the synergism of cell free systems, synthetic bio-circuitry can strive towards improving the standard of living of many of the world’s impoverished.