4.8 Article

TnpB structure reveals minimal functional core of Cas12 nuclease family

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

ColabFold: making protein folding accessible to all

Milot Mirdita et al.

Summary: ColabFold combines fast homology search and optimized model utilization to offer accelerated prediction of protein structures and complexes, with a processing speed that is 40-60 times faster. It serves as a free and accessible platform for protein folding, capable of predicting close to 1,000 structures per day.

NATURE METHODS (2022)

Review Microbiology

Structural biology of CRISPR-Cas immunity and genome editing enzymes

Joy Y. Wang et al.

Summary: CRISPR-Cas systems provide resistance against foreign mobile genetic elements and have a wide range of genome editing and biotechnological applications. This Review examines recent advances in understanding the molecular structures and mechanisms of enzymes comprising bacterial RNA-guided CRISPR-Cas immune systems and deployed for wide-ranging genome editing applications.

NATURE REVIEWS MICROBIOLOGY (2022)

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 Biochemistry & Molecular Biology

Structure of the miniature type V-F CRISPR-Cas effector enzyme

Satoru N. Takeda et al.

Summary: The study reveals that Cas12f1 protein forms a homodimer with a guide RNA to recognize and cleave target DNA, explaining the mechanism of RNA-guided DNA cleavage. Each Cas12f1 protomer plays distinct roles in nucleic acid recognition and DNA cleavage, enhancing the understanding of diverse CRISPR-Cas nucleases.

MOLECULAR CELL (2021)

Article Multidisciplinary Sciences

Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease

Tautvydas Karvelis et al.

Summary: This study reveals that TnpB of Deinococcus radiodurans ISDra2 is an RNA-directed nuclease guided by an RNA from the right-end element of a transposon to cleave DNA next to the 5'-TTGAT transposon-associated motif. The research also demonstrates that TnpB can be reprogrammed to cleave DNA target sites in human cells. These findings highlight the role of TnpB in transposition, confirm that TnpB is a functional precursor of CRISPR-Cas nucleases, and establish TnpB as a prototype for a new genome editing system.

NATURE (2021)

Article Multidisciplinary Sciences

Miniature type V-F CRISPR-Cas nucleases enable targeted DNA modification in cells

Greta Bigelyte et al.

Summary: Class 2 CRISPR systems have diverse effector proteins, with some miniature Cas12f nucleases showing potential for targeted DNA modification in both plant and human cells. The compact size and efficient activity of these Cas12f effectors make them promising tools for in vivo genome editing applications. Biochemical characterization of SpCas12f1 demonstrates its functionality in creating targeted modifications, particularly in plants with short heat pulses.

NATURE COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

Structural basis for substrate recognition and cleavage by the dimerization-dependent CRISPR-Cas12f nuclease

Renjian Xiao et al.

Summary: Cas12f, also known as Cas14, is a small type V-F CRISPR-Cas nuclease with unique substrate recognition and activation mechanisms. Cryo-EM structures revealed an asymmetric Cas12f dimer bound to sgRNA for dsDNA cleavage, highlighting the importance of coordinated conformational changes induced by substrate recognition. Additionally, truncated sgRNA was found to be active for target DNA cleavage, indicating potential genome editing applications for the miniature Cas12f.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Biochemistry & Molecular Biology

DNA interference states of the hypercompact CRISPR-Casφ effector

Patrick Pausch et al.

Summary: Cryo-EM structures of CRISPR-Cas phi, a small RNA-guided enzyme unique to bacteriophages, reveal how Cas phi binds to and cleaves DNA, paving the way for engineering of improved Cas phi variants for diagnostics and genome-editing applications.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

Article Multidisciplinary Sciences

The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases

Han Altae-Tran et al.

Summary: IscB and TnpB, proteins encoded in the IS200/IS605 transposons, are likely ancestors of RNA-guided endonucleases Cas9 and Cas12, respectively, using RNA for DNA cleavage. This study unveils a widespread class of transposon-encoded RNA-guided nucleases, OMEGA, with great potential for biotechnological applications.

SCIENCE (2021)

Article Multidisciplinary Sciences

Structure of the mini-RNA-guided endonuclease CRISPR-Cas12j3

Arturo Carabias et al.

Summary: Researchers have revealed the structure of the CRISPR-Cas12j family and discussed its mechanism in DNA cleavage as well as potential applications in genome editing.

NATURE COMMUNICATIONS (2021)

Review Genetics & Heredity

Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire

Eugene V. Koonin et al.

NATURE REVIEWS GENETICS (2020)

Article Multidisciplinary Sciences

Clades of huge phages from across Earth's ecosystems

Basem Al-Shayeb et al.

NATURE (2020)

Review Microbiology

Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants

Kira S. Makarova et al.

NATURE REVIEWS MICROBIOLOGY (2020)

Article Biochemistry & Molecular Biology

PAM recognition by miniature CRISPR-Cas12f nucleases triggers programmable double-stranded DNA target cleavage

Tautvydas Karvelis et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemical Research Methods

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

Ali Punjani et al.

NATURE METHODS (2020)

Article Biochemical Research Methods

Benchmarking fold detection by DaliLite v.5

Liisa Holm

BIOINFORMATICS (2019)

Article Multidisciplinary Sciences

RNA-guided DNA insertion with CRISPR-associated transposases

Jonathan Strecker et al.

SCIENCE (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

Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a

Daan C. Swarts et al.

MOLECULAR CELL (2019)

Article Multidisciplinary Sciences

CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity

Janice S. Chen et al.

SCIENCE (2018)

Article Biochemical Research Methods

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

Tristan Ian Croll

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a

Isabel Strohkendl et al.

MOLECULAR CELL (2018)

Article Biochemistry & Molecular Biology

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a

Daan C. Swarts et al.

MOLECULAR CELL (2017)

Article Biochemistry & Molecular Biology

Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1

Takashi Yamano et al.

MOLECULAR CELL (2017)

Article Multidisciplinary Sciences

Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage

Stefano Stella et al.

NATURE (2017)

Letter Biotechnology & Applied Microbiology

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

Martin Steinegger et al.

NATURE BIOTECHNOLOGY (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

Addressing preferred specimen orientation in single-particle cryo-EM through tilting

Yong Zi Tan et al.

NATURE METHODS (2017)

Review Microbiology

Diversity and evolution of class 2 CRISPR-Cas systems

Sergey Shmakov et al.

NATURE REVIEWS MICROBIOLOGY (2017)

Article Microbiology

ISC, a Novel Group of Bacterial and Archaeal DNA Transposons That Encode Cas9 Homologs

Vladimir V. Kapitonov et al.

JOURNAL OF BACTERIOLOGY (2016)

Article Biochemistry & Molecular Biology

Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA

Takashi Yamano et al.

Review Biology

Viruses and mobile elements as drivers of evolutionary transitions

Eugene V. Koonin

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2016)

Article Biochemistry & Molecular Biology

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

Bernd Zetsche et al.

Article Biochemical Research Methods

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

Baris E. Suzek et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemical Research Methods

NIH Image to ImageJ: 25 years of image analysis

Caroline A. Schneider et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Features and development of Coot

P. Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemical Research Methods

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Salvador Capella-Gutierrez et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

CLANS: a Java application for visualizing protein families based on pairwise similarity

T Frickey et al.

BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

WebLogo: A sequence logo generator

GE Crooks et al.

GENOME RESEARCH (2004)

Article Biochemistry & Molecular Biology

Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy

PB Rosenthal et al.

JOURNAL OF MOLECULAR BIOLOGY (2003)

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)