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Monitoring SARS-CoV-2 Nsp13 helicase binding activity using expanded genetic code techniques

Lundrigan et al., RSC Chemical Biology, doi:10.1039/d4cb00230j, Apr 2025
https://c19early.org/lundrigan.html
In Vitro study showing that site-specific fluorescent labeling of SARS-CoV-2 Nsp13 helicase enables monitoring of its binding activity with nucleic acid substrates. Authors developed a genetic code expansion technique to incorporate p-azido-L-phenylalanine (AzF) at specific sites in Nsp13, allowing for fluorescent labeling with Cy5-dibenzocyclooctyne (DBCO). They identified two Nsp13-AzF constructs (F81AzF and Y253AzF) that maintained similar unwinding activity to wild-type Nsp13 while enabling efficient fluorescent labeling. Using Förster resonance energy transfer (FRET), they demonstrated that the F81AzF construct could monitor Nsp13 binding to nucleic acid substrates in a distance-dependent manner. This approach provides a novel method for screening potential Nsp13 inhibitors and studying the molecular mechanism of this essential viral helicase during SARS-CoV-2 replication.
Lundrigan et al., 21 Apr 2025, peer-reviewed, 4 authors. Contact: john.pezacki@uottawa.ca.
In Vitro studies are an important part of preclinical research, however results may be very different in vivo.
Monitoring SARS-CoV-2 Nsp13 helicase binding activity using expanded genetic code techniques
Eryn Lundrigan, Christine Hum, Nadine Ahmed, John Paul Pezacki
RSC Chemical Biology, doi:10.1039/d4cb00230j
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) non-structural protein 13 (Nsp13) helicase is a multi-functional protein that can unwind dsDNA and dsRNA in an NTP-dependent manner. Given that this viral helicase is essential for viral replication and highly conserved among coronaviruses, a thorough understanding of the helicase's unwinding and binding activity may allow for the development of more effective pan-coronavirus therapeutics. Herein, we describe the use of genetic code expansion techniques to site-specifically incorporate the non-canonical amino acid (ncAA) p-azido-L-phenylalanine (AzF) into Nsp13 for fluorescent labelling of the enzyme with a conjugated Cy5 fluorophore. This Cy5labelled Nsp13-AzF can then be used in Fo ¨rster resonance energy transfer (FRET) experiments to investigate the dynamics of enzyme translocation on its substrate during binding and unwinding. Five sites (F81, F90, Y205, Y246, and Y253) were identified for AzF incorporation in Nsp13 and assessed for fluorescent labelling efficiency. The incorporation of AzF was confirmed to not interfere with the unwinding activity of the helicase. Subsequently, FRET-based binding assays were conducted to monitor the binding of Cy5-labelled Nsp13-AzF constructs to a series of fluorescently-labelled nucleic acid substrates in a distance-dependent manner. Overall, this approach not only allows for the direct monitoring of Nsp13's binding activity on its substrate, it may also introduce a novel method to screen for compounds that can inhibit this essential enzymatic activity during viral replication.
Author contributions C. Hum performed experimental work, data collection, analysis and writing the original draft. N. Ahmed contributed to conceptualization of the study. E. Lundrigan performed experimental work, data collection, and analysis and contributed to the writing and revising at the stage of review. J. P. Pezacki Conflicts of interest There are no conflicts to declare.
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