Cas nucleases binding selectivity

Cas enzymes have generated significant attention over the past several years, ​mostly for their ability to serve as DNA or RNA targeting platforms, either for manipulation of expression ​of​ single or multiple genes that have been investigated within commercial and academic sectors. To further build upon previously established knowledge of CRISPR binding activity, selectivity and efficiency, we study analytical solutions to first passage times which can be successfully exploited to model binding affinity, and precision, across several Cas nucleases.​​ To achieve more precise computational approximations of first passage times for ​a range of nucleases​ given varying landscape potentials​​, ambient binding temperature, and base pair of inspection against the guide DNA or RNA sequence, we draw upon experimental data gathered for ​spCas9, saCas9, stCas9, asCas12a, and FnCas12a to model CRISPR binding efficiency given selection conditions. To appropriately model the time scales during which DNA or RNA bonds are targeted in successful binding events that minimze off-target impacts, we simulate trajectories of different Cas nucleases throughout genome interrogation and comment upon physical characteristics of the Cas nuclease trajectory, which ultimately determine if binding occurs.