Dynamics and Mechanism of CRISPR systems

CRISPR-Cas9 is a revolutionary genome editing tool, which enables to easily manipulate nucleic acids. Our lab uses computational methods to unravel the function and help the improvement of the CRISPR genome editing machineries. Our multiscale approach is based on large-scale and ab-initio Molecular Dynamics, combined with cryo-EM processing approaches, free energy methods and network models derived on graph theory. This synergistic approach is used to determine the catalysis, allostery and specificity of CRISPR systems.

So far, we described a mechanism for RNA binding and the association with the nucleic acids, and we delivered atomic level details on the off-target effects. We revealed an intriguing mechanism of allosteric regulation and the activation process of the HNH domain. We also established the atomic level details of the catalysis, a fundamental step for the editing of the genome. More exciting research is yet to come! 


[1] Caslino et al. Accepted ACS Catal. 2020. [2] Saha et al. Accepted JCIM 2020. [3] Nierzwicki et al. WIREs Comp Mol Sci Accepted 2020. [4] East K. et al. J. Am. Chem. Soc. 2020. [5] Palermo G. J. Chem. Inf. Model. 2019. [6] Ricci C. G. et al. ACS Cent. Sci. 2019. [7] Palermo G. Chem 2019. [8] Palermo G. et al. Q. Rev. Biophys. 2018. [9] Palermo G. et al. J. Am. Chem. Soc. 2017. [10] Palermo G. et al. Proc. Natl. Acad. Sci. USA, 2017. [11] Palermo G. et al. ACS Cent. Sci. 2016.

Read about the invisible dance of CRISPR-Cas9 in Physics Today