R-loop formation and conformational activation mechanisms of Cas9

Structural basis for mismatch surveillance by CRISPR–Cas9

(2022) Jack P. K. Bravo et al.   NATURE

CRISPR–Cas9 bends and twists DNA to read its sequence

(2022) Joshua C. Cofsky et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement

(2021) Evan A. Boyle et al.   Science Advances

3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM

(2021) Ali Punjani et al.   JOURNAL OF STRUCTURAL BIOLOGY

Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells

(2021) Paul D. Donohoue et al.   MOLECULAR CELL

Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling

(2020) Ivan E. Ivanov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes

(2020) Liyang Zhang et al.   NUCLEIC ACIDS RESEARCH

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity

(2020) Cicera R. Lazzarotto et al.   NATURE BIOTECHNOLOGY

Massively parallel kinetic profiling of natural and engineered CRISPR nucleases

(2020) Stephen K. Jones et al.   NATURE BIOTECHNOLOGY

UCSF ChimeraX : Structure visualization for researchers, educators, and developers

(2020) Eric F. Pettersen et al.   PROTEIN SCIENCE

Catalytic-state structure and engineering of Streptococcus thermophilus Cas9

(2020) Yifei Zhang et al.   Nature Catalysis

Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction

(2020) Ali Punjani et al.   NATURE METHODS

DNA stretching induces Cas9 off-target activity

(2019) Matthew D. Newton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures

(2019) Shuxiang Li et al.   NUCLEIC ACIDS RESEARCH

Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9

(2019) Xing Zhu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

(2019) Dorothee Liebschner et al.   Acta Crystallographica Section D-Structural Biology

Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States

(2019) Wei Sun et al.   MOLECULAR CELL

Target Specificity of Cas9 Nuclease via DNA Rearrangement Regulated by the REC2 Domain

(2018) Keewon Sung et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2018) Mengyi Yang et al.   Cell Reports

Enhanced proofreading governs CRISPR–Cas9 targeting accuracy

(2017) Janice S. Chen et al.   NATURE

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

Mapping the genomic landscape of CRISPR–Cas9 cleavage

(2017) Peter Cameron et al.   NATURE METHODS

Mechanism of duplex DNA destabilization by RNA-guided Cas9 nuclease during target interrogation

(2017) Vladimir Mekler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams et al.   PROTEIN SCIENCE

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

(2017) Yavuz S. Dagdas et al.   Science Advances

Structural Plasticity of PAM Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9

(2016) Carolin Anders et al.   MOLECULAR CELL

High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects

(2016) Benjamin P. Kleinstiver et al.   NATURE

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage

(2016) F. Jiang et al.   SCIENCE

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

(2016) Digvijay Singh et al.   Nature Communications

Two Distinct DNA Binding Modes Guide Dual Roles of a CRISPR-Cas Protein Complex

(2015) Timothy R. Blosser et al.   MOLECULAR CELL

Conformational control of DNA target cleavage by CRISPR–Cas9

(2015) Samuel H. Sternberg et al.   NATURE

A Cas9-guide RNA complex preorganized for target DNA recognition

(2015) F. Jiang et al.   SCIENCE

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

(2014) Hiroshi Nishimasu et al.   CELL

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

(2014) Carolin Anders et al.   NATURE

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

(2014) Samuel H. Sternberg et al.   NATURE

Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

(2014) Cem Kuscu et al.   NATURE BIOTECHNOLOGY

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes

(2014) Mark D. Szczelkun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target

(2014) S. Mulepati et al.   SCIENCE

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Data processing and analysis with theautoPROCtoolbox

(2011) Clemens Vonrhein et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli

(2011) Rimantas Sapranauskas et al.   NUCLEIC ACIDS RESEARCH

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA

(2010) Josiane E. Garneau et al.   NATURE

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS