Molecular Simulations have Boosted Knowledge of CRISPR/Cas9: A Review


  • Angana Ray Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
  • Rosa Di Felice Department of Biological Sciences, Quantitative and Computational Biology Sector, University of Southern California, Los Angeles, CA 90089, USA



CRISPR/Cas9, genome editing, computer simulations, molecular dynamics, structure-function relationship.


Genome editing allows scientists to change an organism’s DNA. One promis-
ing genome editing protocol, already validated in living organisms, is based
on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas
protein-nucleic acid complexes. When the CRISPR/Cas approach was first
demonstrated in 2012, its advantages with respect to previously available
techniques, such as zinc-finger nucleases (ZFNs) and transcription activator-
like effector nucleases (TALENs), immediately got attention and the method
has seen a surge of experimental and computational investigations since then.
However, the molecular mechanisms involved in target DNA recognition and
cleavage are still not completely resolved and need further attention. The large
size and complex nature of CRISPR/Cas9 complexes has been a challenge
for computational studies, but some seed results exist and are illuminating
on the cleavage activity. In this short review, we present recent progress
in studying CRISPR/Cas9 systems by molecular dynamics simulations with
coarse-grained and atomistic descriptions, including enhanced sampling.


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Author Biographies

Angana Ray, Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA

Angana Ray received her PhD in Chemistry in 2016 at Saha Institute of
Nuclear Physics, India, where she studied the Structure and Dynamics of
Biomolecular Systems (DNA, RNA and proteins). She joined the University
of Southern California in Los Angeles as a postdoc in the Department of
Physics and Astronomy in 2018 and is working on CRISPR/Cas systems. Her
specific research interest is on understanding protein-nucleic acid complexes
by Molecular Dynamics simulations.

Rosa Di Felice, Department of Biological Sciences, Quantitative and Computational Biology Sector, University of Southern California, Los Angeles, CA 90089, USA

Rosa Di Felice received her PhD in Physics in 1996 at the University of Rome
“Tor Vergata”, Italy. She is a member of the research staff in the Italian National
Research Council (CNR previously INFM) in Modena, Italy, since 2001, and an Associate Professor at the University of Southern California since 2013.
She is an author of about 120 peer reviewed articles, including letters and
reviews. Her current research interests focus on the theoretical/computational
investigation of biological macromolecules and their interactions with other
biological molecules and inorganic nanoparticles. She is also exploring the
use of noisy intermediate state quantum computers in quantum chemistry.


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How to Cite

Ray, A., & Felice, R. D. (2023). Molecular Simulations have Boosted Knowledge of CRISPR/Cas9: A Review. Journal of Self Assembly and Molecular Electronics, 7(1), 45–72.