Ribozymes: Methods and Protocols

✍ Scribed by Robert J Scarborough, Anne Gatignol

• Publisher: Springer US;Humana
• Year: 2021
• Tongue: English
• Leaves: 300
• Series: Methods in Molecular Biology 2167
• Edition: 1st ed.
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

Front Matter ....Pages i-xi
Front Matter ....Pages 1-1
Conjugation as a Highly Sensitive Assay to Study Group II Intron Splicing In Vivo (Félix LaRoche-Johnston, Caroline Monat, Benoit Cousineau)....Pages 3-11
Co-transcriptional Analysis of Self-Cleaving Ribozymes and Their Ligand Dependence (Luiz F. M. Passalacqua, Andrej Lupták)....Pages 13-24
Front Matter ....Pages 25-25
Cloning and Detection of Genomic Retrozymes and Their circRNA Intermediates (Amelia Cervera, Marcos de la Peña)....Pages 27-44
Demonstration of a Ribozyme in Epsilon Domain of Hepatitis B Virus RNA (Dibyajnan Chakraborty, Sagarmoy Ghosh)....Pages 45-59
In Vitro Selection of Varkud Satellite Ribozyme Variants that Cleave a Modified Stem-Loop Substrate (Pierre Dagenais, Pascale Legault)....Pages 61-77
Characterization and Optimization of a Deoxyribozyme with a Short Left Binding Arm (Yueyao Wang, Hanyang Yu)....Pages 79-89
Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes (Sabrine Najeh, Kasra Zandi, Samia Djerroud, Nawwaf Kharma, Jonathan Perreault)....Pages 91-111
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
Front Matter ....Pages 145-145
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
SHAPE Profiling to Probe Group II Intron Conformational Dynamics During Splicing (Timothy Wiryaman, Navtej Toor)....Pages 171-182
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
Front Matter ....Pages 203-203
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
Design and Evaluation of AgoshRNAs with 3′-Terminal HDV Ribozymes to Enhance the Silencing Activity (Ben Berkhout, Elena Herrera-Carrillo)....Pages 225-252
Cloning and Detection of Aptamer-Ribozyme Conjugations (Ryan P. Goguen, Anne Gatignol, Robert J. Scarborough)....Pages 253-267
Front Matter ....Pages 269-269
Use of a Lariat Capping Ribozyme to Study Cap Function In Vivo (Max Pietschmann, Gregor Tempel, Maral Halladjian, Nicolai Krogh, Henrik Nielsen)....Pages 271-285
Long Non-coding RNA Depletion Using Self-Cleaving Ribozymes (Alex C. Tuck, Marc Bühler)....Pages 287-301
Correction to: Using an L7Ae-Tethered, Hydroxyl Radical-Mediated Footprinting Strategy to Identify and Validate Kink-Turns in RNAs (Stella M. Lai, Venkat Gopalan)....Pages C1-C1
Back Matter ....Pages 303-304

✦ Subjects

Biomedicine; Human Genetics