CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations

Significance The CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9) system recently emerged as a transformative genome editing technology that is innovating life science, with cutting-edge impact in biomedicine, pharmaceutics, and agriculture. Nevertheless, the molecular mechanism underlying CRISPR-Cas9 function is still incompletely understood. Here, enhanced molecular dynamics (MD) simulations, probing displacements over long timescales, capture at atomic level specific features that are difficult to reach via conventional MD simulations and via the currently available experimental techniques, clarifying the molecular mechanism of CRISPR-Cas9, with understanding of its activation process. The insights obtained from our molecular simulations provide key reference points for future experimental studies of CRISPR-Cas9 and its applications as a genome editing tool.