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CRISPR

Methods and Protocols

  • Book
  • © 2015

Overview

Editors:
  1. Magnus Lundgren

    1. Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden

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  2. Emmanuelle Charpentier

    1. Department of Molecular Biology MIMS, Umeå University, Umeå, Sweden

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    You can also search for this editor in PubMed   Google Scholar

  3. Peter C. Fineran

    1. Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1311)

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About this book

This volume presents a list of cutting-edge protocols for the study of CRISPR-Cas defense systems and their applications at the genomic, genetic, biochemical and structural levels. CRISPR: Methods and Protocols guides readers through techniques that have been developed specifically for the analysis of CRISPR-Cas and techniques adapted from standard protocols of DNA, RNA and protein biology. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, CRISPR: Methods and Protocols provides a broad list of tools and techniques to study the interdisciplinary aspects of the prokaryotic CRISPR-Cas defense systems.

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Table of contents (23 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Investigating CRISPR RNA Biogenesis and Function Using RNA-seq

    • Nadja Heidrich, Gaurav Dugar, Jörg Vogel, Cynthia M. Sharma
    Pages 1-21

  3. In Vitro Co-reconstitution of Cas Protein Complexes

    • André Plagens, Lennart Randau
    Pages 23-33

  4. Analysis of CRISPR Pre-crRNA Cleavage

    • Erin L. Garside, Andrew M. MacMillan
    Pages 35-46

  5. Annotation and Classification of CRISPR-Cas Systems

    • Kira S. Makarova, Eugene V. Koonin
    Pages 47-75

  6. Computational Detection of CRISPR/crRNA Targets

    • Ambarish Biswas, Peter C. Fineran, Chris M. Brown
    Pages 77-89

  7. High-Throughput CRISPR Typing of Mycobacterium tuberculosis Complex and Salmonella enterica Serotype Typhimurium

    • Christophe Sola, Edgar Abadia, Simon Le Hello, François-Xavier Weill
    Pages 91-109

  8. Spacer-Based Macroarrays for CRISPR Genotyping

    • Igor Mokrousov, Nalin Rastogi
    Pages 111-131

  9. Analysis of crRNA Using Liquid Chromatography Electrospray Ionization Mass Spectrometry (LC ESI MS)

    • Sakharam P. Waghmare, Alison O. Nwokeoji, Mark J. Dickman
    Pages 133-145

  10. Rapid Multiplex Creation of Escherichia coli Strains Capable of Interfering with Phage Infection Through CRISPR

    • Alexandra Strotksaya, Ekaterina Semenova, Ekaterina Savitskaya, Konstantin Severinov
    Pages 147-159

  11. Exploring CRISPR Interference by Transformation with Plasmid Mixtures: Identification of Target Interference Motifs in Escherichia coli

    • Cristóbal Almendros, Francisco J. M. Mojica
    Pages 161-170

  12. Electrophoretic Mobility Shift Assay of DNA and CRISPR-Cas Ribonucleoprotein Complexes

    • Tim Künne, Edze R. Westra, Stan J. J. Brouns
    Pages 171-184

  13. Expression and Purification of the CMR (Type III-B) Complex in Sulfolobus solfataricus

    • Jing Zhang, Malcolm F. White
    Pages 185-194

  14. Procedures for Generating CRISPR Mutants with Novel Spacers Acquired from Viruses or Plasmids

    • Marie-Ève Dupuis, Rodolphe Barrangou, Sylvain Moineau
    Pages 195-222

  15. Archaeal Viruses of the Sulfolobales: Isolation, Infection, and CRISPR Spacer Acquisition

    • Susanne Erdmann, Roger A. Garrett
    Pages 223-232

  16. Using the CRISPR-Cas System to Positively Select Mutants in Genes Essential for Its Function

    • Ido Yosef, Moran G. Goren, Rotem Edgar, Udi Qimron
    Pages 233-250

  17. Analysis of Nuclease Activity of Cas1 Proteins Against Complex DNA Substrates

    • Natalia Beloglazova, Sofia Lemak, Robert Flick, Alexander F. Yakunin
    Pages 251-264

  18. Characterizing Metal-Dependent Nucleases of CRISPR-Cas Prokaryotic Adaptive Immunity Systems

    • Ki H. Nam, Matthew P. DeLisa, Ailong Ke
    Pages 265-276

  19. Cas3 Nuclease–Helicase Activity Assays

    • Tomas Sinkunas, Giedrius Gasiunas, Virginijus Siksnys
    Pages 277-291

  20. Chemical and Enzymatic Footprint Analyses of R-Loop Formation by Cascade-crRNA Complex

    • Ümit Pul
    Pages 293-305
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Editors and Affiliations

  • Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden

    Magnus Lundgren

  • Department of Molecular Biology MIMS, Umeå University, Umeå, Sweden

    Emmanuelle Charpentier

  • Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand

    Peter C. Fineran

Bibliographic Information

  • Book Title: CRISPR

  • Book Subtitle: Methods and Protocols

  • Editors: Magnus Lundgren, Emmanuelle Charpentier, Peter C. Fineran

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-2687-9

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2015

  • Hardcover ISBN: 978-1-4939-2686-2Published: 20 May 2015

  • Softcover ISBN: 978-1-4939-5428-5Published: 09 October 2016

  • eBook ISBN: 978-1-4939-2687-9Published: 18 May 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 366

  • Number of Illustrations: 26 b/w illustrations, 37 illustrations in colour

  • Topics: Gene Expression

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