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Ribozymes

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Robert J Scarborough

    1. Department of Microbiology and Immunology, Lady Davis Institute for Medical Research, Montréal, Canada

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    You can also search for this editor in PubMed   Google Scholar

  2. Anne Gatignol

    1. Department of Microbiology and Immunology, Lady Davis Institute for Medical Research, Montréal, Canada

    View editor publications

    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 2167)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
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  2. Ribozyme Function

    1. Front Matter

      Pages 1-1
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    2. Conjugation as a Highly Sensitive Assay to Study Group II Intron Splicing In Vivo

      • Félix LaRoche-Johnston, Caroline Monat, Benoit Cousineau
      Pages 3-11

    3. Co-transcriptional Analysis of Self-Cleaving Ribozymes and Their Ligand Dependence

      • Luiz F. M. Passalacqua, Andrej Lupták
      Pages 13-24

  3. Ribozyme Identification and Characterization

    1. Front Matter

      Pages 25-25
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    2. Cloning and Detection of Genomic Retrozymes and Their circRNA Intermediates

      • Amelia Cervera, Marcos de la Peña
      Pages 27-44

    3. Demonstration of a Ribozyme in Epsilon Domain of Hepatitis B Virus RNA

      • Dibyajnan Chakraborty, Sagarmoy Ghosh
      Pages 45-59

    4. In Vitro Selection of Varkud Satellite Ribozyme Variants that Cleave a Modified Stem-Loop Substrate

      • Pierre Dagenais, Pascale Legault
      Pages 61-77

    5. Characterization and Optimization of a Deoxyribozyme with a Short Left Binding Arm

      • Yueyao Wang, Hanyang Yu
      Pages 79-89

    6. Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes

      • Sabrine Najeh, Kasra Zandi, Samia Djerroud, Nawwaf Kharma, Jonathan Perreault
      Pages 91-111

    7. Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots

      • Mohammad Kayedkhordeh, Ryota Yamagami, Philip C. Bevilacqua, David H. Mathews
      Pages 113-143

  4. Ribozyme Structure

    1. Front Matter

      Pages 145-145
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    2. Using an L7Ae-Tethered, Hydroxyl Radical-Mediated Footprinting Strategy to Identify and Validate Kink-Turns in RNAs

      • Stella M. Lai, Venkat Gopalan
      Pages 147-169

    3. SHAPE Profiling to Probe Group II Intron Conformational Dynamics During Splicing

      • Timothy Wiryaman, Navtej Toor
      Pages 171-182

    4. Dynamics-Function Analysis in Catalytic RNA Using NMR Spin Relaxation and Conformationally Restricted Nucleotides

      • Charles G. Hoogstraten, Montserrat Terrazas, Anna Aviñó, Neil A. White, Minako Sumita
      Pages 183-202

  5. Ribozyme Conjugations

    1. Front Matter

      Pages 203-203
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    2. Design and Evaluation of Guide RNA Transcripts with a 3′-Terminal HDV Ribozyme to Enhance CRISPR-Based Gene Inactivation

      • Ben Berkhout, Zongliang Gao, Elena Herrera-Carrillo
      Pages 205-224

    3. Design and Evaluation of AgoshRNAs with 3′-Terminal HDV Ribozymes to Enhance the Silencing Activity

      • Ben Berkhout, Elena Herrera-Carrillo
      Pages 225-252

    4. Cloning and Detection of Aptamer-Ribozyme Conjugations

      • Ryan P. Goguen, Anne Gatignol, Robert J. Scarborough
      Pages 253-267

  6. Ribozyme as Tools to Study Other RNAs

    1. Front Matter

      Pages 269-269
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Keywords

About this book

This volume provides protocols designed to study the function and the structure of diverse ribozymes. Chapters guide readers through different techniques to identify and characterize new ribozymes and methods to use ribozymes to alter the function of CRISPR-based guide RNAs, AgoshRNAs and aptamers or to study RNA capping and long non-coding RNAs. 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, Ribozymes: Methods and Protocols aims to help in accelerating ribozyme research and inspiring others to develop new methods to study ribozyme structure and function.


Editors and Affiliations

  • Department of Microbiology and Immunology, Lady Davis Institute for Medical Research, Montréal, Canada

    Robert J Scarborough, Anne Gatignol

Bibliographic Information

  • Book Title: Ribozymes

  • Book Subtitle: Methods and Protocols

  • Editors: Robert J Scarborough, Anne Gatignol

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0716-9

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

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

  • Hardcover ISBN: 978-1-0716-0715-2Published: 26 July 2020

  • Softcover ISBN: 978-1-0716-0718-3Published: 27 July 2021

  • eBook ISBN: 978-1-0716-0716-9Published: 25 July 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 304

  • Number of Illustrations: 29 b/w illustrations, 43 illustrations in colour

  • Topics: Human Genetics

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