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CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations
Experiments with structural & mechanistic focus.
DNA interrogation by the CRISPR RNA-guided endonuclease Cas9
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Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips
Cas9 domain fluctuations by FRET
Structures and mechanisms by Cryo-EM Cell 2017
Biophysical models of specificity.
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https://www.nature.com/articles/srep37584.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110985/
QM:MM Simulations
Gamess+Tinker http://cfm.ehu.es/ricardo/master/intranet_ESCMAN/WinGAMESS/manuals/simomm.pdf (advantages: free, disadvantages: might not run well )
Gaussian+Gromacs http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM (advantages: will work well, Scuseria will likely help; disadvantages: will likely be limited to Rice U comp. resources.)
Mechanistic Insight into Catalytic Activity of BBA-Metallonucleases (This model system, Vibrio vulnificus, is thought to have the same cleavage mechanism as the HNH domain.)
Catalytic Mechanisms of Restriction and Homing Endonucleases (A general overview of both one- and two-metal reactions, not specifically theory-oriented.)
The Nucleophile in Ribozyme Catalysis (Not directly related, but an analogous cleavage reaction. The SI also has lots of detailed information on their QM/MM simulations.)
RNA coarse grain models:
http://pubs.acs.org/doi/abs/10.1021/jp104926t
http://rnajournal.cshlp.org/content/14/6/1164.long
Layman news:
https://www.wired.com/2017/06/crispr-mutations
https://hms.harvard.edu/news/bringing-crispr-focus