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CRISPR Guide RNA Design

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Tudor A. Fulga

    1. Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK

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  2. David J. H. F. Knapp

    1. Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK

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    You can also search for this editor in PubMed   Google Scholar

  3. Quentin R. V. Ferry

    1. Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2162)

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Table of contents (15 protocols)

  1. Front Matter

    Pages i-x
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  2. In Silico Design and Optimization of Guide RNA Sequences

    1. Front Matter

      Pages 1-1
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    2. Cloud-Based Design of Short Guide RNA (sgRNA) Libraries for CRISPR Experiments

      • Florian Heigwer, Michael Boutros
      Pages 3-22

    3. Web-Based CRISPR Toolkits: Cas-OFFinder, Cas-Designer, and Cas-Analyzer

      • Gue-Ho Hwang, Jin-Soo Kim, Sangsu Bae
      Pages 23-33

  3. Chemically-Modified Guide RNAs

    1. Front Matter

      Pages 35-35
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    2. Chemical Modification of Guide RNAs for Improved CRISPR Activity in CD34+ Human Hematopoietic Stem and Progenitor Cells

      • Jenny Shapiro, Adi Tovin, Ortal Iancu, Daniel Allen, Ayal Hendel
      Pages 37-48

    3. Gene Disruption Using Chemically Modified CRISPR-Cpf1 RNA

      • Moira A. McMahon, Meghdad Rahdar
      Pages 49-60

    4. “Split-and-Click” sgRNA

      • Lapatrada Taemaitree, Arun Shivalingam, Afaf H. El-Sagheer, Tom Brown
      Pages 61-78

    5. Chimeric DNA–RNA Guide RNA Designs

      • Shuhan Lu, Ying Zhang, Hao Yin
      Pages 79-85

  5. Characterization of CRISPR Efficacy and Specificity

    1. Front Matter

      Pages 195-195
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    2. Methods for Measuring CRISPR/Cas9 DNA Cleavage in Cells

      • Christopher R. Cromwell, Juan Jovel, Basil P. Hubbard
      Pages 197-213

    3. In Vitro Assays for Comparing the Specificity of First- and Next-Generation CRISPR/Cas9 Systems

      • Christopher R. Cromwell, Basil P. Hubbard
      Pages 215-232

    4. Profiling Genome-Wide Specificity of CRISPR-Cas9 Using Digenome-Seq

      • Daesik Kim, Jin-Soo Kim
      Pages 233-242

    5. Detection of CRISPR/Cas9-Generated Off-Target Effect by Integration-Defective Lentiviral Vector

      • Xiaoling Wang, Youjun Wu, Jiing-Kuan Yee
      Pages 243-260

    6. Genome-Wide CRISPR Off-Target DNA Break Detection by the BLISS Method

      • Roberto Ballarino, Britta A. M. Bouwman, Nicola Crosetto
      Pages 261-281
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Keywords

About this book

This detailed volume focuses on the CRISPR-associated guide RNA and how it can be designed, modified, and validated for a broad repertoire of purposes. Beginning with a section on computational design of target-specific guide RNAs, the book continues by covering chemical modifications to alter guide RNA stability, specificity, and efficiency, as well as to create inducible guide RNAs, append additional functional domains, and express guide RNAs in a conditional manner. It concludes with methods for measuring off-target guide RNA activity. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and essential, CRISPR Guide RNA Design: Methods and Protocols provides a comprehensive pipeline for guide RNA design and aims to be an invaluable resource in applying this powerful technology to basic research and therapeutic applications.

Editors and Affiliations

  • Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK

    Tudor A. Fulga, David J. H. F. Knapp, Quentin R. V. Ferry

Bibliographic Information

  • Book Title: CRISPR Guide RNA Design

  • Book Subtitle: Methods and Protocols

  • Editors: Tudor A. Fulga, David J. H. F. Knapp, Quentin R. V. Ferry

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0687-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-0686-5Published: 15 September 2020

  • Softcover ISBN: 978-1-0716-0689-6Published: 16 September 2021

  • eBook ISBN: 978-1-0716-0687-2Published: 14 September 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 286

  • Number of Illustrations: 10 b/w illustrations, 46 illustrations in colour

  • Topics: Genetics and Genomics, Biomedical Engineering and Bioengineering

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