Single molecule characterization of the activity of an enzyme and its inhibitors involved in SARS-CoV-2 replication

The helicase Nsp13 is the RNA unwinding molecular motor of the SARS-CoV-2 and it is essential for its replication.
While it is one of the most conserved protein among the coronovirus family (100% similarity of the helicase sequence between SARS-CoV-1, SARS-CoV-2 and Mers-CoV), its functional properties still remain badly understood, the main reason being that standard bulk experiments offer poor characterization of this type of DNA/RNA unwinding molecular motors.

Indeed, when an helicase translocates on a duplex nucleic acid (dNA), the duplex can refold behindthe helicase, thus preventing the observation of the dynamics of the enzyme with standard electrophoresis gels. Such methods only allow the observation of the action of the enzyme on very short substrates (roughly 20 bp) that cannot refold after the passage of the enzyme, and thus fail to describe accurately the dynamics of the motor (processivity, velocity, sequence-induced pauses, strand switches …).

Furthermore, their conclusions are often ambiguous as the observed and quantified dehybridization of short duplexes may happen spontaneously during the binding of the helicase through the melting of a few bases, and is thus not a completely reliable proxy of unwinding activity.

Building on the strong expertise of our consortium in the field of single-molecule helicase studies (and in particular
about Upf1, a human helicase structurally very similar to Nsp13), we wish to provide the community working on the virus with a precise functional characterization of the enzyme.

By describing functional properties of the helicase of the virus that can only be observed through single-molecules
measurements, this project thus aims to :

– quickly unveil a poorly understood member of the proteome of the virus that is essential for the virus dissemination.
– validate ~10 potential therapeutic pathways targeting the helicase.