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Items: 1 to 20 of 96


Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics.

Ricci CG, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA, Palermo G.

ACS Cent Sci. 2019 Apr 24;5(4):651-662. doi: 10.1021/acscentsci.9b00020. Epub 2019 Mar 7.


Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain.

Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA.

Q Rev Biophys. 2018;51. pii: e91. doi: 10.1017/S0033583518000070. Epub 2018 Aug 3.


CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations.

Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA.

Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):7260-7265. doi: 10.1073/pnas.1707645114. Epub 2017 Jun 26. Erratum in: Proc Natl Acad Sci U S A. 2017 Oct 17;114(42):E8944.


The Conformational Dynamics of Cas9 Governing DNA Cleavage Are Revealed by Single-Molecule FRET.

Yang M, Peng S, Sun R, Lin J, Wang N, Chen C.

Cell Rep. 2018 Jan 9;22(2):372-382. doi: 10.1016/j.celrep.2017.12.048.


Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9.

Palermo G, Ricci CG, Fernando A, Basak R, Jinek M, Rivalta I, Batista VS, McCammon JA.

J Am Chem Soc. 2017 Nov 15;139(45):16028-16031. doi: 10.1021/jacs.7b05313. Epub 2017 Aug 7.


Structure and Dynamics of the CRISPR-Cas9 Catalytic Complex.

Palermo G.

J Chem Inf Model. 2019 May 28;59(5):2394-2406. doi: 10.1021/acs.jcim.8b00988. Epub 2019 Feb 27.


A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9.

Dagdas YS, Chen JS, Sternberg SH, Doudna JA, Yildiz A.

Sci Adv. 2017 Aug 4;3(8):eaao0027. doi: 10.1126/sciadv.aao0027. eCollection 2017 Aug.


Conformational control of DNA target cleavage by CRISPR-Cas9.

Sternberg SH, LaFrance B, Kaplan M, Doudna JA.

Nature. 2015 Nov 5;527(7576):110-3. doi: 10.1038/nature15544. Epub 2015 Oct 28.


Structure and Dynamics of Cas9 HNH Domain Catalytic State.

Zuo Z, Liu J.

Sci Rep. 2017 Dec 8;7(1):17271. doi: 10.1038/s41598-017-17578-6.


Protospacer adjacent motif (PAM)-distal sequences engage CRISPR Cas9 DNA target cleavage.

Cencic R, Miura H, Malina A, Robert F, Ethier S, Schmeing TM, Dostie J, Pelletier J.

PLoS One. 2014 Oct 2;9(10):e109213. doi: 10.1371/journal.pone.0109213. eCollection 2014.


Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations.

Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA.

ACS Cent Sci. 2016 Oct 26;2(10):756-763. Epub 2016 Sep 9.


CRISPR-Cas9 Structures and Mechanisms.

Jiang F, Doudna JA.

Annu Rev Biophys. 2017 May 22;46:505-529. doi: 10.1146/annurev-biophys-062215-010822. Epub 2017 Mar 30. Review.


Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9.

Singh D, Sternberg SH, Fei J, Doudna JA, Ha T.

Nat Commun. 2016 Sep 14;7:12778. doi: 10.1038/ncomms12778.


A Broad-Spectrum Inhibitor of CRISPR-Cas9.

Harrington LB, Doxzen KW, Ma E, Liu JJ, Knott GJ, Edraki A, Garcia B, Amrani N, Chen JS, Cofsky JC, Kranzusch PJ, Sontheimer EJ, Davidson AR, Maxwell KL, Doudna JA.

Cell. 2017 Sep 7;170(6):1224-1233.e15. doi: 10.1016/j.cell.2017.07.037. Epub 2017 Aug 24.


DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.

Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA.

Nature. 2014 Mar 6;507(7490):62-7. doi: 10.1038/nature13011. Epub 2014 Jan 29.


Structural insights into DNA cleavage activation of CRISPR-Cas9 system.

Huai C, Li G, Yao R, Zhang Y, Cao M, Kong L, Jia C, Yuan H, Chen H, Lu D, Huang Q.

Nat Commun. 2017 Nov 9;8(1):1375. doi: 10.1038/s41467-017-01496-2.


CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences.

Lin Y, Cradick TJ, Brown MT, Deshmukh H, Ranjan P, Sarode N, Wile BM, Vertino PM, Stewart FJ, Bao G.

Nucleic Acids Res. 2014 Jun;42(11):7473-85. doi: 10.1093/nar/gku402. Epub 2014 May 16.


Dynamics changes of CRISPR-Cas9 systems induced by high fidelity mutations.

Zheng L, Shi J, Mu Y.

Phys Chem Chem Phys. 2018 Nov 7;20(43):27439-27448. doi: 10.1039/c8cp04226h.


Bidirectional Degradation of DNA Cleavage Products Catalyzed by CRISPR/Cas9.

Stephenson AA, Raper AT, Suo Z.

J Am Chem Soc. 2018 Mar 14;140(10):3743-3750. doi: 10.1021/jacs.7b13050. Epub 2018 Feb 20.


Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease.

Anders C, Niewoehner O, Duerst A, Jinek M.

Nature. 2014 Sep 25;513(7519):569-73. doi: 10.1038/nature13579. Epub 2014 Jul 27.

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