Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations

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dc.creatorZuo, Zhicheng
dc.creatorLiu, Jin
dc.creator.orcid0000-0002-1067-4063 (Liu, Jin)
dc.date.accessioned2022-09-30T17:34:18Z
dc.date.available2022-09-30T17:34:18Z
dc.date.issued2016-11-22
dc.description.abstractThe CRISPR-associated endonuclease Cas9 from Streptococcus pyogenes (spCas9) along with a single guide RNA (sgRNA) has emerged as a versatile toolbox for genome editing. Despite recent advances in the mechanism studies on spCas9-sgRNA-mediated double-stranded DNA (dsDNA) recognition and cleavage, it is still unclear how the catalytic Mg(2+) ions induce the conformation changes toward the catalytic active state. It also remains controversial whether Cas9 generates blunt-ended or staggered-ended breaks with overhangs in the DNA. To investigate these issues, here we performed the first all-atom molecular dynamics simulations of the spCas9-sgRNA-dsDNA system with and without Mg(2+) bound. The simulation results showed that binding of two Mg(2+) ions at the RuvC domain active site could lead to structurally and energetically favorable coordination ready for the non-target DNA strand cleavage. Importantly, we demonstrated with our simulations that Cas9-catalyzed DNA cleavage produces 1-bp staggered ends rather than generally assumed blunt ends.
dc.identifier.citationZuo, Z., & Liu, J. (2016). Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations. Scientific reports, 5, 37584. https://doi.org/10.1038/srep37584
dc.identifier.issn2045-2322
dc.identifier.urihttps://hdl.handle.net/20.500.12503/31822
dc.identifier.volume5
dc.publisherSpringer Nature
dc.relation.urihttps://doi.org/10.1038/srep37584
dc.rights.holder© The Author(s) 2016
dc.rights.licenseAttribution 4.0 International (CC BY 4.0)
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.sourceScientific Reports
dc.subject.meshBacterial Proteins / chemistry
dc.subject.meshBacterial Proteins / genetics
dc.subject.meshCRISPR-Associated Protein 9
dc.subject.meshCatalytic Domain
dc.subject.meshCations, Monovalent
dc.subject.meshDNA / chemistry
dc.subject.meshDNA / genetics
dc.subject.meshDNA Cleavage
dc.subject.meshEndonucleases / chemistry
dc.subject.meshEndonucleases / genetics
dc.subject.meshMagnesium / chemistry
dc.subject.meshMolecular Dynamics Simulation
dc.subject.meshRNA, Guide / chemistry
dc.titleCas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations
dc.typeArticle
dc.type.materialtext

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