Our lab applies and develops advanced computer simulations to uncover the molecular mechanisms and engineer new genome editing systems. By integrating computational methods with deep learning we aim to deepen our understanding and revolutionize the design of gene editors. Our approach includes graph neural networks (GNNs), diffusion and language models, seemingly combined with molecular dynamics, quantum mechanics, and cryo-electron microscopy (cryo-EM) processing techniques. Our findings are integrated with experimental techniques, including cryo-EM, single-molecule spectroscopy, and NMR.
Selected Publications
2025: A. C. Patel, S. Sinha, P. R. Arantes and G. Palermo.† Unveiling Cas8 Dynamics and Regulation within a transposon-encoded Cascade-TniQ Complex. 2025 Proc. Natl. Acad. Sci. USA, 122, e2422895122.
2024: A. Saha, M. Ahsan,* P. R. Arantes,* M. Schmitz, C. Chanez, M. Jinek and G. Palermo.† An Alpha-helical Lid Guides the Target DNA toward Catalysis in CRISPR-Cas12a. 2024 Nat. Commun. 15, 1473.
2023: S. Sinha, A. M. Molina Vargas, P. R. Arantes,* A. Patel,* M R. O’Connell.† and G. Palermo.† Unveiling the RNA-mediated allosteric activation discloses functional hotspots in CRISPR-Cas13a. Nucleic Acids Res. 2023, gkad1127.
2022: Ł. Nierzwicki, K. W. East, J. Binz, R. V. Hsu, M. Ahsan, P. R. Arantes, E. Skeens, M. Pacesa, M. Jinek, G. P. Lisi† and G. Palermo.† Principles of Target DNA Cleavage and Role of Mg2+ in the Catalysis of CRISPR-Cas9. Nature Catal. 2022, 5, 912-922. PDF
2021: Ł. Nierzwicki, K. W. East, U. N. Morzan, P. R. Arantes, V. S. Batista, G. P. Lisi† and G. Palermo.† Enhanced Specificity Mutations Perturb Allosteric Signaling in CRISPR-Cas9. eLife 2021, 10: e73601.
2020: L. Casalino, Ł. Nierzwicki, M. Jinek and G. Palermo.† Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab-Initio Molecular Dynamics. ACS Catalysis, 2020, 22, 13596-13605.
2019: C. G. Ricci, J. S. Chen, Y. Miao, M. Jinek, J. A. Doudna, J. A. McCammon and G. Palermo.† Deciphering Off-target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. ACS Cent. Sci. 2019, 5, 651-662.
Palermo Lab 