The CRISPR/Cas9 system
is a popular genome-editing tool with immense
therapeutic potential. It is a simple two-component system (Cas9 protein
and RNA) that recognizes the DNA sequence on the basis of RNA:DNA
complementarity, and the Cas9 protein catalyzes the double-stranded
break in the DNA. In the past decade, near-atomic resolution structures
at various stages of the CRISPR/Cas9 DNA editing pathway have been
reported along with numerous experimental and computational studies.
Such studies have boosted knowledge of the genome-editing mechanism.
Despite such advancements, the application of CRISPR/Cas9 in therapeutics
is still limited, primarily due to off-target effects. Several studies
aim at engineering high-fidelity Cas9 to minimize the off-target effects.
Molecular Dynamics (MD) simulations have been an excellent complement
to the experimental studies for investigating the mechanism of CRISPR/Cas9
editing in terms of structure, thermodynamics, and kinetics. MD-based
studies have uncovered several important molecular aspects of Cas9,
such as nucleotide binding, catalytic mechanism, and off-target effects.
In this Review, the contribution of MD simulation to understand the
CRISPR/Cas9 mechanism has been discussed, preceded by an overview
of the history, mechanism, and structural aspects of the CRISPR/Cas9
system. These studies are important for the rational design of highly
specific Cas9 and will also be extremely promising for achieving more
accurate genome editing in the future.