Catalytic amplification by transition-state molecular switches for direct and sensitive detection of SARS-CoV-2

Sundah, Noah R.; Natalia, Auginia; Liu, Yu; Ho, Nicholas R. Y.; Zhao, Haitao; Chen, Yuan; Miow, Qing Hao; Wang, Yu; Beh, Darius L. L.; Chew, Ka Lip; Chan, Douglas; Tambyah, Paul A.; Ong, Catherine W. M.; Shao, Huilin

Despite the importance of nucleic acid testing in managing the COVID-19 pandemic, current detection approaches remain limited due to their high complexity and extensive processing. Here, we describe a molecular nanotechnology that enables direct and sensitive detection of viral RNA targets in native clinical samples. The technology, termed catalytic amplification by transition-state molecular switch (CATCH), leverages DNA-enzyme hybrid complexes to form a molecular switch. By ratiometric tuning of its constituents, the multicomponent molecular switch is prepared in a hyperresponsive state—the transition state—that can be readily activated upon the binding of sparse RNA targets to turn on substantial enzymatic activity. CATCH thus achieves superior performance (~8 RNA copies/μl), direct fluorescence detection that bypasses all steps of PCR (<1 hour at room temperature), and versatile implementation (high-throughput 96-well format and portable microfluidic assay). When applied for clinical COVID-19 diagnostics, CATCH demonstrated direct and accurate detection in minimally processed patient swab samples.