Giulia Palermo, Aiding SARS-CoV-2 detection through emerging CRISPR-Cas genome editing technologies

Giulia Palermo, UC Riverside.
October 20, 2020. 3:35 – 4:50 pm.
A Joint Virtual Seminar with IIT’s Chemistry Colloquium on Blackboard Collaborate.

The SARS-CoV-2 coronavirus is rapidly spreading across multiple countries, causing a severe acute respiratory syndrome that threatens the world population. As the number of cases is steadily growing, there is pressing need for rapid testing tools, which could limit the contagion. New versions of the CRISPR gene-editing system are being harnessed as a fast, yet reliable diagnostic tool against SARS-CoV-2 infections. However, the molecular basis of viral nucleic acid detection is largely elusive, demanding improved approaches to expedite detection. Here, we describe how the CRISPR-associated protein Cas12a recognizes viral genetic material through microsecond-long simulations. Molecular simulations of CRISPR-Cas12a reveal that DNA binding induces a switch in the conformational dynamics of the Cas12a protein, which results in the activation of the peripheral REC2 and Nuc domains to enable cleavage of nucleic acids. Accordingly, large-amplitude motions of the Nuc domain favor the conformational activation of the system toward DNA cleavages, while the joint dynamics of REC2 is shown to prime the conformational transition of the DNA target strand toward the catalytic site. Most notably, the highly coupled dynamics of the REC2 region and Nuc domain suggest that REC2 could act as a regulator of the Nuc function, similar to what was observed previously for the HNH domain in the CRISPR-associated nuclease Cas9. Considering that the REC lobe is a key determinant in the system’s specificity, our findings provide a rational basis for future biophysical studies aimed at characterizing its function in CRISPR-Cas12a. Overall, the dynamic and mechanistic aspects reported here are at the bottleneck in the process of detecting viral nucleic acids, delivering information that can help in expediting detection. This is the utmost need of the time considering the increasing number of afflicted individuals. 

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