Arantes PR - Search Results

1

Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes.

Wang J, Arantes PR, Ahsan M, Sinha S, Kyro GW, Maschietto F, Allen B, Skeens E, Lisi GP, Batista VS, Palermo G. Wang J, et al. Among authors: arantes pr. Front Mol Biosci. 2023 Jan 9;9:1072733. doi: 10.3389/fmolb.2022.1072733. eCollection 2022. Front Mol Biosci. 2023. PMID: 36699705 Free PMC article. Review.

2

Structural basis for Cas9 off-target activity.

Pacesa M, Lin CH, Cléry A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M. Pacesa M, et al. Among authors: arantes pr. Cell. 2022 Oct 27;185(22):4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Cell. 2022. PMID: 36306733 Free PMC article.

3

GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems.

Kumar A, Arantes PR, Saha A, Palermo G, Wong BM. Kumar A, et al. Among authors: arantes pr. Molecules. 2023 Jan 28;28(3):1277. doi: 10.3390/molecules28031277. Molecules. 2023. PMID: 36770943 Free PMC article.

4

Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR-Cas9.

Nierzwicki Ł, East KW, Binz JM, Hsu RV, Ahsan M, Arantes PR, Skeens E, Pacesa M, Jinek M, Lisi GP, Palermo G. Nierzwicki Ł, et al. Among authors: arantes pr. Nat Catal. 2022 Oct;5(10):912-922. doi: 10.1038/s41929-022-00848-6. Epub 2022 Oct 6. Nat Catal. 2022. PMID: 36778082 Free PMC article.

5

Machines on Genes through the Computational Microscope.

Sinha S, Pindi C, Ahsan M, Arantes PR, Palermo G. Sinha S, et al. Among authors: arantes pr. J Chem Theory Comput. 2023 Apr 11;19(7):1945-1964. doi: 10.1021/acs.jctc.2c01313. Epub 2023 Mar 22. J Chem Theory Comput. 2023. PMID: 36947696 Free PMC article. Review.

6

RNA-mediated Allosteric Activation in CRISPR-Cas13a.

Sinha S, Molina Vargas AM, Arantes PR, Patel A, O'Connell MR, Palermo G. Sinha S, et al. Among authors: arantes pr. bioRxiv [Preprint]. 2023 Jul 27:2023.07.27.550797. doi: 10.1101/2023.07.27.550797. bioRxiv. 2023. PMID: 37546822 Free PMC article. Updated. Preprint.

7

Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease.

Wang J, Maschietto F, Qiu T, Arantes PR, Skeens E, Palermo G, Lisi GP, Batista VS. Wang J, et al. Among authors: arantes pr. Biophys J. 2023 Dec 19;122(24):4635-4644. doi: 10.1016/j.bpj.2023.11.005. Epub 2023 Nov 7. Biophys J. 2023. PMID: 37936350

8

Unveiling the RNA-mediated allosteric activation discloses functional hotspots in CRISPR-Cas13a.

Sinha S, Molina Vargas AM, Arantes PR, Patel A, O'Connell MR, Palermo G. Sinha S, et al. Among authors: arantes pr. Nucleic Acids Res. 2024 Jan 25;52(2):906-920. doi: 10.1093/nar/gkad1127. Nucleic Acids Res. 2024. PMID: 38033317 Free PMC article.

9

New design strategies for ultra-specific CRISPR-Cas13a-based RNA detection with single-nucleotide mismatch sensitivity.

Molina Vargas AM, Sinha S, Osborn R, Arantes PR, Patel A, Dewhurst S, Hardy DJ, Cameron A, Palermo G, O'Connell MR. Molina Vargas AM, et al. Among authors: arantes pr. Nucleic Acids Res. 2024 Jan 25;52(2):921-939. doi: 10.1093/nar/gkad1132. Nucleic Acids Res. 2024. PMID: 38033324 Free PMC article.

10

An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a.

Saha A, Ahsan M, Arantes PR, Schmitz M, Chanez C, Jinek M, Palermo G. Saha A, et al. Among authors: arantes pr. Nat Commun. 2024 Feb 17;15(1):1473. doi: 10.1038/s41467-024-45762-6. Nat Commun. 2024. PMID: 38368461 Free PMC article.

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