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CRISPR-Cas Enzymes, Volume 616, the latest release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Topics covered in this release include CRISPR bioinformatics, A method for one-step assembly of Class 2 CRISPR arrays, Biochemical reconstitution and structural analysis of ribonucleoprotein complexes in Type I-E CRISPR-Cas systems, Mechanistic dissection of the CRISPR interference pathway in Type I-E CRISPR-Cas system, Site-specific fluorescent labeling of individual proteins within CRISPR complexes, Fluorescence-based methods for measuring target interference by CRISPR-Cas systems, Native State Structural Characterization of CRISRP Associated Complexes using Mass Spectrometry, and more.
List of contents
1. Predicting and visualizing features of CRISPR-Cas systems
Matthew A. Nethery and Rodolphe Barrangou
2. Reconstitution and biochemical characterization of ribonucleoprotein complexes in Type I-E CRISPR-Cas systems
Yibei Xiao and Ailong Ke
3. Sortase-mediated fluorescent labeling of CRISPR complexes
Kaylee E. Dillard, Jeffrey M. Schaub, Maxwell W. Brown, Fatema A. Saifuddin, Yibei Xiao, Erik Hernandez, Samuel D. Dahlhauser, Eric V. Anslyn, Ailong Ke and Ilya J. Finkelstein
4. Fluorescence-based methods for measuring target interference by CRISPR-Cas systems
Phong T. Phan, Michael Schelling, Chaoyou Xue and Dipali G. Sashital
5. Probing Cascade complex composition and stability using native mass spectrometry techniques
Angela Patterson, Monika Tokmina-Lukaszewska and Brian Bothner
6. High-throughput determination of in vivo DNA sequence preferences for Cas protein binding using Library-ChIP
Joseph T. Wade
7. Live-cell single-particle tracking photoactivated localization microscopy of Cascade-mediated DNA surveillance
Bartosz Turkowyd, Hanna Müller-Esparza, Vanessa Climenti, Niklas Steube, Ulrike Endesfelder and Lennart Randau
8. In vitro assembly of thermostable Csm complex in CRISPR-Cas type III/A system
Kwang-Hyun Park, Yan An and Eui-Jeon Woo
9. Investigation of the cyclic oligoadenylate signaling pathway of type III CRISPR systems
Christophe Rouillon, Januka S. Athukoralage, Shirley Graham, Sabine Grüschow and Malcolm F. White
10. A pipeline for characterization of novel Cas9 orthologs
Tautvydas Karvelis, Joshua K. Young and Virginijus Siksnys
11. Preparation and electroporation of Cas12a/Cpf1-guide RNA complexes for introducing large gene deletions in mouse embryonic stem cells
Lucas Kissling, Asun Monfort, Daan C. Swarts, Anton Wutz and Martin Jinek
12. Directed evolution studies of a thermophilic Type II-C Cas9
Travis H. Hand, Anuska Das and Hong Li
13. Kinetic characterization of Cas9 enzymes
Mu-Sen Liu, Shanzhong Gong, Helen-Hong Yu, David W. Taylor and Kenneth A. Johnson
14. Single-molecule FRET studies of Cas9 endonuclease
Viktorija Globyte and Chirlmin Joo
15. CRISPR-Cas molecular beacons as tool for studies of assembly of CRISPR-Cas effector complexes and their interactions with DNA
Vladimir Mekler, Konstantin Kuznedelov, Leonid Minakhin, Karthik Murugan, Dipali G. Sashital and Konstantin Severinov
16. Adapting dCas9-APEX2 for subnuclear proteomic profiling
Xin D. Gao, Tomás C. Rodríguez and Erik J. Sontheimer
17. CRISPR-Cas10 assisted editing of virulent staphylococcal phages
S.M. Nayeemul Bari and Asma Hatoum-Aslan
18. Reconstitution of CRISPR adaptation in vitro and its detection by PCR
Robert D. Fagerlund, Timothy J. Ferguson, Howard W.R. Maxwell, Helen K. Opel-Reading, Kurt L. Krause and Peter C. Fineran
About the author
Scott Bailey is at Johns Hopkins Bloomberg School of Public Health, USA
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