4.8 Article

R-loop formation and conformational activation mechanisms of Cas9

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

Structural basis for mismatch surveillance by CRISPR-Cas9

Jack P. K. Bravo et al.

Summary: In this study, the structure of Cas9 during mismatch cleavage was determined using kinetics-guided cryo-electron microscopy. It was found that a linear conformation of the guide RNA-DNA duplex formed in the presence of mismatches, preventing Cas9 activation. Additionally, mismatches distal to the protospacer adjacent motif were stabilized by reorganization of a loop in the RuvC domain. Mutations of mismatch-stabilizing residues reduced off-target DNA cleavage while maintaining rapid on-target DNA cleavage. This study provides proof of concept for the design of next-generation high-fidelity Cas9 variants targeting mismatch tolerance regions.

NATURE (2022)

Article Biochemistry & Molecular Biology

CRISPR-Cas9 bends and twists DNA to read its sequence

Joshua C. Cofsky et al.

Summary: Researchers have discovered that the Cas9 protein bends and twists DNA when binding to PAM, allowing DNA nucleotides to be extracted from the double helix and examined by the guide RNA. This finding is significant for understanding the efficiency of genome editing.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2022)

Article Biotechnology & Applied Microbiology

Massively parallel kinetic profiling of natural and engineered CRISPR nucleases

Stephen K. Jones et al.

Summary: The study compares the specificity and cleavage outcomes of engineered and natural nucleases using a massively parallel platform called NucleaSeq, which combines nucleases digestion and deep sequencing. Engineered Cas9s, especially Cas9-HF1, show increased cleavage specificity but not binding specificity compared to wild-type Cas9, while surprisingly AsCas12a cleavage specificity differs little from that of wild-type Cas9. The study also reveals that initial DNA cleavage sites and end trimming vary by nuclease, guide RNA, and the positions of mispaired nucleotides.

NATURE BIOTECHNOLOGY (2021)

Article Biochemistry & Molecular Biology

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

Eric F. Pettersen et al.

Summary: UCSF ChimeraX is a powerful visualization program with enhanced performance and graphics, offering new tools and analysis features, support for various areas like virtual reality, and improved ease of use, along with an app store for researchers to contribute new tools.

PROTEIN SCIENCE (2021)

Article Multidisciplinary Sciences

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

Evan A. Boyle et al.

Summary: Through high-throughput experiments, researchers observed significant variations in binding and cleavage efficacy, as well as specificity, of Cas9 ribonucleoproteins (RNPs) across different guide RNAs. Canonical guide sequences often exhibit unusually high specificity, and the sequence context surrounding the target modulates the Cas9 on-rate. Furthermore, Cas9 RNPs may trap targets in non-productive states that contribute to proofreading capability.

SCIENCE ADVANCES (2021)

Article Biochemistry & Molecular Biology

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

Ali Punjani et al.

Summary: 3DVA is an algorithm that fits a linear subspace model of conformational change to high-resolution cryo-EM data, enabling the resolution and visualization of detailed molecular motions of proteins. It has been shown to successfully resolve multiple flexible motions in various protein complexes, providing new biological insights from single particle cryo-EM data.

JOURNAL OF STRUCTURAL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

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

Paul D. Donohoue et al.

Summary: Research shows that using CRISPR hybrid RNA-DNA guides (chRDNA) can improve Cas9 specificity and reduce off-target effects. By experimenting on multiple genomic targets in human T cells, researchers found that the positioning of 2'-deoxynucleotides impacts guide activity and specificity, allowing for the design of effective chRDNA guides.

MOLECULAR CELL (2021)

Article Multidisciplinary Sciences

Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling

Ivan E. Ivanov et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biochemistry & Molecular Biology

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

Liyang Zhang et al.

NUCLEIC ACIDS RESEARCH (2020)

Review Biotechnology & Applied Microbiology

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

Andrew V. Anzalone et al.

NATURE BIOTECHNOLOGY (2020)

Article Biotechnology & Applied Microbiology

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

Cicera R. Lazzarotto et al.

NATURE BIOTECHNOLOGY (2020)

Article Chemistry, Physical

Catalytic-state structure and engineering of Streptococcus thermophilus Cas9

Yifei Zhang et al.

NATURE CATALYSIS (2020)

Article Biochemical Research Methods

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

Ali Punjani et al.

NATURE METHODS (2020)

Article Biochemistry & Molecular Biology

DNA stretching induces Cas9 off-target activity

Matthew D. Newton et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)

Article Biochemistry & Molecular Biology

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

Shuxiang Li et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

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

Xing Zhu et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)

Article Biochemical Research Methods

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

Dorothee Liebschner et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

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

Christopher J. Williams et al.

PROTEIN SCIENCE (2018)

Article Chemistry, Multidisciplinary

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

Keewon Sung et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

Article Biochemistry & Molecular Biology

Helix-7 in Argonaute2 shapes the microRNA seed region for rapid target recognition

Shannon M. Klum et al.

EMBO JOURNAL (2018)

Article Multidisciplinary Sciences

Enhanced proofreading governs CRISPR-Cas9 targeting accuracy

Janice S. Chen et al.

NATURE (2017)

Article Biochemical Research Methods

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

Ali Punjani et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

Mapping the genomic landscape of CRISPR-Cas9 cleavage

Peter Cameron et al.

NATURE METHODS (2017)

Article Multidisciplinary Sciences

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

Vladimir Mekler et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Multidisciplinary Sciences

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

Yavuz S. Dagdas et al.

SCIENCE ADVANCES (2017)

Article Biochemistry & Molecular Biology

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

Carolin Anders et al.

MOLECULAR CELL (2016)

Article Multidisciplinary Sciences

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

Benjamin P. Kleinstiver et al.

NATURE (2016)

Article Biotechnology & Applied Microbiology

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

John G. Doench et al.

NATURE BIOTECHNOLOGY (2016)

Article Multidisciplinary Sciences

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

Fuguo Jiang et al.

SCIENCE (2016)

Article Multidisciplinary Sciences

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

Digvijay Singh et al.

NATURE COMMUNICATIONS (2016)

Article Biochemistry & Molecular Biology

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

Timothy R. Blosser et al.

MOLECULAR CELL (2015)

Article Multidisciplinary Sciences

Conformational control of DNA target cleavage by CRISPR-Cas9

Samuel H. Sternberg et al.

NATURE (2015)

Article Multidisciplinary Sciences

A Cas9-guide RNA complex preorganized for target DNA recognition

Fuguo Jiang et al.

SCIENCE (2015)

Article Biotechnology & Applied Microbiology

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

Shengdar Q. Tsai et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemistry & Molecular Biology

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

Hiroshi Nishimasu et al.

Article Multidisciplinary Sciences

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

Carolin Anders et al.

NATURE (2014)

Article Multidisciplinary Sciences

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

Samuel H. Sternberg et al.

NATURE (2014)

Article Biotechnology & Applied Microbiology

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

Cem Kuscu et al.

NATURE BIOTECHNOLOGY (2014)

Article Multidisciplinary Sciences

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

Mark D. Szczelkun et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

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

Sabin Mulepati et al.

SCIENCE (2014)

Article Biotechnology & Applied Microbiology

DNA targeting specificity of RNA-guided Cas9 nucleases

Patrick D. Hsu et al.

NATURE BIOTECHNOLOGY (2013)

Article Multidisciplinary Sciences

RNA-Guided Human Genome Engineering via Cas9

Prashant Mali et al.

SCIENCE (2013)

Article Multidisciplinary Sciences

Multiplex Genome Engineering Using CRISPR/Cas Systems

Le Cong et al.

SCIENCE (2013)

Article Biology

RNA-programmed genome editing in human cells

Martin Jinek et al.

Article Multidisciplinary Sciences

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

Martin Jinek et al.

SCIENCE (2012)

Article Biochemical Research Methods

Data processing and analysis with the autoPROC toolbox

Clemens Vonrhein et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

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

Rimantas Sapranauskas et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemical Research Methods

Features and development of Coot

P. Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Multidisciplinary Sciences

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

Josiane E. Garneau et al.

NATURE (2010)

Article Biochemical Research Methods

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

Andrew M. Waterhouse et al.

BIOINFORMATICS (2009)

Review Biochemistry & Molecular Biology

Inference of macromolecular assemblies from crystalline state

Evgeny Krissinel et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Biochemistry & Molecular Biology

MUSCLE: multiple sequence alignment with high accuracy and high throughput

RC Edgar

NUCLEIC ACIDS RESEARCH (2004)