RNA structures principally defined by their base-pairing potentials, are vital determinants of several natural regulatory networks. This dependence on base-pairing to form specific structures, and the structure's role in controlling translation has also been exploited for synthetic networks. We have engineered SARS-CoV-2 RNA biosensors from an existing synthetic scaffold called the Toehold RNA. Toehold RNAs can be tailored to switch in response to a specific target RNA sequence. In the absence of target RNA, translation of the downstream lacZ/nano-lantern reporter gene is blocked by the RNA structure, Translation significantly increases in the presence of target RNA, which opens up the structure, exposing the ribosome binding site making it conducive for translation. This results in lacZ production which is detected by the cleavage of a chromogenic substrate- thus resulting in an RNA biosensor that produces colour in the presence of SARS-CoV-2 RNA.

By combining our biosensor with isothermally amplified SARS-CoV-2 RNA, as few as 100 copies of SARS-CoV-2 RNA can be detected. This assay is thus useful in detecting COVID in a majority of patient samples. A colour readout discernable by eye and quantifiable through smart phones makes detection possible even in remote settings. By employing a different reporter – nano-lantern, we can get a lumiscence based readout, which is faster compared to colour development.

Regulation of translation by RNA scaffolds appears to be a common theme recurring widely in nature, from prokaryotes to eukaryotes, and viruses. Identifying and understanding these natural RNA regulatory elements will further our grasp on the nuances of regulation. I will talk about a few such examples of natural regulatory elements.