RAPID: Enzyme-free detection of coronavirus RNA using reconfigurable DNA nanoswitches

Engineering - A critical aspect of controlling the current COVID-19 outbreaks is early and fast detection of the infected population. Current methods for detecting the novel coronavirus that causes COVID-19 typically require a laboratory and use expensive equipment and reagents. These requirements limit the number of tests that can be performed nationwide. In this project, the research team aims to develop an alternative diagnostic approach that directly detects the viral RNA without any amplification, labeling, or the use of enzymes. The assay requires minimal steps and uses a compact, bufferless gel cartridge system that can be deployed in a clinical setting. Beyond the current COVID-19 outbreak, this sensing platform can also apply to other existing or emerging viruses.

This work aims to develop a nanoswitch assay sensitive enough to detect clinical levels of SARS-CoV-2 viral RNA within 1 hour. Once the viral RNA is extracted from a sample, the RNA is fragmented and mixed with the DNA-based nanoswitches. Hybridization of a viral RNA fragment of a specific sequence with a nanoswitch induces a conformational change of the engineered DNA strand from its linear "off" state to a looped "on" state. After separation of the target-bound looped form from the linear nanoswitches by electrophoresis in a gel cartridge system, the viral load is quantified from the intensity of the looped (on) nanoswitches in a gel image.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.