tRNA mimicking structures to control and monitor biological processes
Most of the bacterial switches are cis encoded lacking the versatility with respect to input signals. These cis encoded switches may interfere with folding of the downstream mRNA. To overcome this problem, we present versatile and modular RNA switches that are trans encoded and based on tRNA‐mimicking structures (TMSs). These switches can be designed to accept a wide range of inputs, including RNA, small molecules, and proteins. Being trans encoded, these switches do not require to alter upstream genetic sequences and thus it helps to mitigate the problem of losing necessary regulatory elements. We also engineered the tRNA mimicking structure (TMS) under control of small photo-switchable signaling molecules. The light responsiveness of our system originates from the photo-switchable noncovalent interactions between the signaling molecule and the TMS switch, leading to the demonstration of photochemically controlled expression of different genes. After realizing the potential of the RNA based switch, we have introduced a trans encoded ssDNA switch by simply converting the RNA based TMS switch into its deoxynucleotide analogue. The ssDNA switch was constructed using the Ec86 retron that produces ssDNA by reverse transcriptase (RT). The ssDNA switch accommodates different type of inputs (RNA and small molecules). We also present an entirely genetically encoded RNA-based sensor with a modular design feature that allows straightforward repurposing towards new analytes. The sensor does not require exogenous ligands and is instead based on turn-on fluorescence as analyte-binding releases GFP. This method has the potential to be a standard tool for analyte detection in cells.