TnpB structure reveals minimal functional core of Cas12 nuclease family

[1]  A. Ke,et al.  Structural basis for RNA-guided DNA cleavage by IscB-ωRNA and mechanistic comparison with Cas9 , 2022, Science.

[2]  J. Doudna,et al.  Structural biology of CRISPR–Cas immunity and genome editing enzymes , 2022, Nature Reviews Microbiology.

[3]  Joshua K Young,et al.  Miniature type V-F CRISPR-Cas nucleases enable targeted DNA modification in cells , 2021, Nature Communications.

[4]  Č. Venclovas,et al.  Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease , 2021, Nature.

[5]  Suchita P. Nety,et al.  The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases , 2021, Science.

[6]  S. Ovchinnikov,et al.  ColabFold: making protein folding accessible to all , 2022, Nature Methods.

[7]  J. Banfield,et al.  DNA interference states of the hypercompact CRISPR–CasΦ effector , 2021, Nature Structural & Molecular Biology.

[8]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[9]  T. Pape,et al.  Structure of the mini-RNA-guided endonuclease CRISPR-Cas12j3 , 2021, Nature Communications.

[10]  Leifu Chang,et al.  Structural basis for substrate recognition and cleavage by the dimerization-dependent CRISPR–Cas12f nuclease , 2021, Nucleic acids research.

[11]  H. Nishimasu,et al.  Structure of the miniature type V-F CRISPR-Cas effector enzyme. , 2020, Molecular cell.

[12]  Conrad C. Huang,et al.  UCSF ChimeraX: Structure visualization for researchers, educators, and developers , 2020, Protein science : a publication of the Protein Society.

[13]  Joshua K Young,et al.  PAM recognition by miniature CRISPR–Cas12f nucleases triggers programmable double-stranded DNA target cleavage , 2020, Nucleic acids research.

[14]  Stan J. J. Brouns,et al.  Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants , 2019, Nature Reviews Microbiology.

[15]  David J. Fleet,et al.  Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction , 2019, Nature Methods.

[16]  Liisa Holm,et al.  Benchmarking fold detection by DaliLite v.5 , 2019, Bioinform..

[17]  E. Koonin,et al.  Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire , 2019, Nature Reviews Genetics.

[18]  Randy J. Read,et al.  Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix , 2019, Acta crystallographica. Section D, Structural biology.

[19]  Eugene V Koonin,et al.  RNA-guided DNA insertion with CRISPR-associated transposases , 2019, Science.

[20]  Christine L. Sun,et al.  Clades of huge phages from across Earth’s ecosystems , 2019, bioRxiv.

[21]  D. C. Swarts,et al.  Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a. , 2019, Molecular cell.

[22]  Johannes Thomsen,et al.  Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity , 2018, Cell.

[23]  James R. Rybarski,et al.  Kinetic basis for DNA target specificity of CRISPR-Cas12a , 2018, bioRxiv.

[24]  Jennifer A. Doudna,et al.  CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity , 2018, Science.

[25]  Tristan Ian Croll,et al.  ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps , 2018, Acta crystallographica. Section D, Structural biology.

[26]  Johannes Söding,et al.  MMseqs2: sensitive protein sequence searching for the analysis of massive data sets , 2017, bioRxiv.

[27]  H. Nishimasu,et al.  Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1. , 2017, Molecular cell.

[28]  Joseph H. Davis,et al.  Addressing preferred specimen orientation in single-particle cryo-EM through tilting , 2017, Nature Methods.

[29]  S. Stella,et al.  Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage , 2017, Nature.

[30]  D. C. Swarts,et al.  Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a. , 2017, Molecular cell.

[31]  David J. Fleet,et al.  cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination , 2017, Nature Methods.

[32]  Kira S. Makarova,et al.  Diversity and evolution of class 2 CRISPR–Cas systems , 2017, Nature Reviews Microbiology.

[33]  E. Koonin Viruses and mobile elements as drivers of evolutionary transitions , 2016, Philosophical Transactions of the Royal Society B: Biological Sciences.

[34]  D. Patel,et al.  Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition , 2016, Cell Research.

[35]  Kira S. Makarova,et al.  Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA , 2016, Cell.

[36]  E. Koonin,et al.  ISC, a Novel Group of Bacterial and Archaeal DNA Transposons That Encode Cas9 Homologs , 2015, Journal of bacteriology.

[37]  A. Regev,et al.  Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System , 2015, Cell.

[38]  Peter B. McGarvey,et al.  UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches , 2014, Bioinform..

[39]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[40]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[41]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[42]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[43]  Andrei N. Lupas,et al.  CLANS: a Java application for visualizing protein families based on pairwise similarity , 2004, Bioinform..

[44]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[45]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[46]  R. Henderson,et al.  Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. , 2003, Journal of molecular biology.