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  • Garneau, J. E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67–71 (2010).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Sapranauskas, R. et al. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res. 39, 9275–9282 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Jinek, M. et al. RNA-programmed genome editing in human cells. eLife 2, e00471 (2013).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Mekler, V., Minakhin, L. & Severinov, K. Mechanism of duplex DNA destabilization by RNA-guided Cas9 nuclease during target interrogation. Proc. Natl Acad. Sci. USA 114, 5443–5448 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C. & Doudna, J. A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62–67 (2014).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Szczelkun, M. D. et al. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. Proc. Natl Acad. Sci. USA 111, 9798–9803 (2014).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Anders, C., Niewoehner, O., Duerst, A. & Jinek, M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513, 569–573 (2014).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Ivanov, I. E. et al. Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling. Proc. Natl Acad. Sci. USA 117, 5853–5860 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Jiang, F., Zhou, K., Ma, L., Gressel, S. & Doudna, J. A. A Cas9–guide RNA complex preorganized for target DNA recognition. Science 348, 1477–1481 (2015).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Sternberg, S. H., LaFrance, B., Kaplan, M. & Doudna, J. A. Conformational control of DNA target cleavage by CRISPR–Cas9. Nature 527, 110–113 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Cameron, P. et al. Mapping the genomic landscape of CRISPR–Cas9 cleavage. Nat. Methods 14, 600–606 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR–Cas9. Nat. Biotechnol. 34, 184–191 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Hsu, P. D. et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31, 827–832 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Lazzarotto, C. R. et al. CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity. Nat. Biotechnol. 38, 1317–1327 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR–Cas nucleases. Nat. Biotechnol. 33, 187–197 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Boyle, E. A. et al. Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement. Sci. Adv. 7, eabe5496 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Jones, S. K. Jr et al. Massively parallel kinetic profiling of natural and engineered CRISPR nucleases. Nat. Biotechnol. 39, 84–93 (2021).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • Zhang, L. et al. Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes. Nucleic Acids Res. 48, 5037–5053 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Singh, D., Sternberg, S. H., Fei, J., Doudna, J. A. & Ha, T. Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9. Nat. Commun. 7, 12778 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Chen, J. S. et al. Enhanced proofreading governs CRISPR–Cas9 targeting accuracy. Nature 550, 407–410 (2017).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Dagdas, Y. S., Chen, J. S., Sternberg, S. H., Doudna, J. A. & Yildiz, A. A conformational checkpoint between DNA binding and cleavage by CRISPR–Cas9. Sci. Adv. 3, eaao0027 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Anders, C., Bargsten, K. & Jinek, M. Structural plasticity of PAM recognition by engineered variants of the RNA-guided endonuclease Cas9. Mol. Cell. 61, 895–902 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Jiang, F. et al. Structures of a CRISPR–Cas9 R-loop complex primed for DNA cleavage. Science 351, 867–871 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935–949 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Zhu, X. et al. Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9. Nat. Struct. Mol. Biol. 26, 679–685 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Punjani, A. & Fleet, D. J. 3D variability analysis: resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM. J. Struct. Biol. 213, 107702 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Cofsky, J. C., Soczek, K. M., Knott, G. J., Nogales, E. & Doudna, J. A. CRISPR–Cas9 bends and twists DNA to read its sequence. Nat. Struct. Mol. Biol. 29, 395–402 (2022).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Sung, K., Park, J., Kim, Y., Lee, N. K. & Kim, S. K. Target specificity of Cas9 nuclease via DNA rearrangement regulated by the REC2 domain. J. Am. Chem. Soc. 140, 7778–7781 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Kleinstiver, B. P. et al. High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529, 490–495 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Yang, M. et al. The conformational dynamics of Cas9 governing DNA cleavage are revealed by single-molecule FRET. Cell Rep. 22, 372–382 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Sun, W. et al. Structures of Neisseria meningitidis Cas9 complexes in catalytically poised and anti-CRISPR-inhibited states. Mol. Cell 76, 938–952 e935 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Zhang, Y. et al. Catalytic-state structure and engineering of Streptococcus thermophilus Cas9. Nat. Catal. 3, 813–823 (2020).

    CAS 
    Article 

    Google Scholar 

  • Casalino, L., Nierzwicki, L., Jinek, M. & Palermo, G. Catalytic mechanism of non-target DNA cleavage in CRISPR–Cas9 revealed by ab initio molecular dynamics. ACS Catal. 10, 13596–13605 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Bravo, J. P. K. et al. Structural basis for mismatch surveillance by CRISPR–Cas9. Nature 603, 343–347 (2022).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Klum, S. M., Chandradoss, S. D., Schirle, N. T., Joo, C. & MacRae, I. J. Helix-7 in Argonaute2 shapes the microRNA seed region for rapid target recognition. EMBO J. 37, 75–88 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Mulepati, S., Heroux, A. & Bailey, S. Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target. Science 345, 1479–1484 (2014).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Blosser, T. R. et al. Two distinct DNA binding modes guide dual roles of a CRISPR–Cas protein complex. Mol. Cell 58, 60–70 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Xiao, Y. et al. Structure basis for directional R-loop formation and substrate handover mechanisms in type I CRISPR–Cas system. Cell 170, 48–60 e11 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Kuscu, C., Arslan, S., Singh, R., Thorpe, J. & Adli, M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat. Biotechnol. 32, 677–683 (2014).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Anzalone, A. V., Koblan, L. W. & Liu, D. R. Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 38, 824–844 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Pacesa, M. et al. Structural basis for Cas9 off-target activity. Preprint at bioRxiv https://doi.org/10.1101/2021.11.18.469088 (2021).

  • Donohoue, P. D. et al. Conformational control of Cas9 by CRISPR hybrid RNA–DNA guides mitigates off-target activity in T cells. Mol. Cell 81, 3637–3649.e3635 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Newton, M. D. et al. DNA stretching induces Cas9 off-target activity. Nat. Struct. Mol. Biol. 26, 185–192 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Vonrhein, C. et al. Data processing and analysis with the autoPROC toolbox. Acta Crystallogr. D 67, 293–302 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).

    CAS 
    Article 

    Google Scholar 

  • Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Methods 17, 1214–1221 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Li, S., Olson, W. K. & Lu, X. J. Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures. Nucleic Acids Res. 47, W26–W34 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M. & Barton, G. J. Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 



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