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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.
List of contents
Conjugation as a Highly Sensitive Assay to Study Group II Intron Splicing in vivo.- Co-transcriptional Analysis of Self-cleaving Ribozymes and their Ligand Dependence.- Cloning and Detection of Genomic Retrozymes and their circRNA Intermediates.- Demonstration of a Ribozyme in Epsilon Domain of Hepatitis B Virus RNA.- In vitro Selection of Varkud Satellite Ribozyme Variants that Cleave a Modified Stem-loop Substrate.- Characterization and Optimization of a Deoxyribozyme with a Short Left Binding Arm.- Computer-aided Design of Active Pseudoknotted Hammerhead Ribozymes.- Inverse RNA Folding Workflow to Design and Test Ribozymes Including Pseudoknots.- Using an L7Ae-tethered, Hydroxyl Radical-Mediated Footprinting Strategy to Identify and Validate Kink-Turns in RNAs.- SHAPE Profiling to Probe Group II Intron Conformational Dynamics during Splicing.- Dynamics-Function Analysis in Catalytic RNA Using NMR Spin Relaxation and Conformationally Restricted Nucleotides.- Design and Evaluation of Guide RNA Transcripts with a 3'-terminal HDV Ribozyme to Enhance CRISPR-based Gene Inactivation.- Design and Evaluation of AgoshRNAs with 3'-terminal HDV Ribozymes to Enhance the Silencing Activity.- Cloning and Detection of Aptamer-ribozyme Conjugations.- Use of a Lariat Capping Ribozyme to Study Cap Function in Vivo.- Long Non-coding RNA Depletion using Self-cleaving Ribozymes.
