IISER researchers devlop strategy to enhance RNA-based biosensors’ sensitivity

The work was funded by the Shastri Indo-Canadian Institute (SICI) and an international consortium supported by the International Development Research Centre (IDRC), Government of Canada.

Think of a toehold switch like a smoke detector. Normally, it’s silent (no signal), but when it detects smoke (viral RNA), it triggers an alarm (colour change). The researchers upgraded the detector to be more sensitive, like making it spot even a tiny whiff of smoke faster and louder, so it’s easier to notice without complex equipment.

“The approach taken uses a technique referred to as ‘toehold switches’, that has previously been demonstrated to be successful for the detection of molecular signatures of viruses and other pathogens. These are programmable ribonucleic acid (RNA) sequences which, in presence of viral RNA, will produce a color signal due to a combination of enzyme production and colored substrate – thus serving as a “genetic device,” Athale said.

Such devices are promising for low-cost, portable diagnostics in low-resource settings, as shown in the previous work from Dr Pardee’s research group during the Zika virus outbreak in Brazil. One limitation in this previous approach was the number of steps involved in obtaining sufficient signal amplification.

In this collaborative study, the researchers addressed this limitation by incorporating short genetic sequences known as “translational enhancers” upstream of the toehold region, resulting in increased protein expression upon target detection.”The improved sensors were tested using RNA sequences from SARS-CoV-2 and Zika virus (ZIKV), and successfully validated in cell-free systems. This potentially points to a proof-of-concept of a paper-disc based molecular diagnostic test, relevant for point-of-care (PoC) use in low-resource environments,” Athale added.

According to Athale they will aim to expand the scope of viruses that can be detected, build a software pipeline to speed up the design process and reduce the cost of fine chemicals that are required to be ordered. “We are aiming at improving our ability to detect by eye, something closer to the rapid antigen test for home use. There are many scientific challenges still to be resolved, and we hope for support for these, since we believe the work has societal benefit,” he added.