Theory and computation early career award talk: unraveling the CRISPR-Cas revolution through the lens of computational biophysics.

Abstract

The clustered regularly interspaced short palindromic repeat (CRISPR) genome-editing revolution established the beginning of a new era in life sciences. I will report the role of state-of-the-art computations in the CRISPR-Cas9 revolution, from the early refinement of cryo-EM data to enhanced simulations of large-scale conformational transitions. Molecular simulations reported a mechanism for RNA binding and the formation of a catalytically competent Cas9 enzyme, corroborated by recent cryo-EM data of the activated state. Inspired by single-molecule experiments, molecular dynamics offered a rationale for the onset of off-target effects, while graph theory unveiled the allosteric regulation. Finally, the use of a mixed quantum-classical approach established the catalytic mechanism of DNA cleavage. Overall, molecular simulations have been instrumental in understanding the dynamics and mechanism of CRISPR-Cas9, contributing to understanding function, catalysis, allostery, and specificity. Future computational studies will bridge the scales from quantum mechanical approaches to enhanced simulations and cryo-EM processing methods to push the boundaries of molecular simulations and tackle the most exciting problems in the biophysics of genome editing.