Ribozymes, Softcover reprint of the original 1st ed. 2012 Methods and Protocols Methods in Molecular Biology Series, Vol. 848

Over the past decade, there have been a variety of fundamental insights into ribozymes which have changed the perspective on RNA catalysis. In, Ribozymes: Methods and Protocols, researchers in the field detail many of the protocols and techniques which are now commonly used to study individual ribozymes and the characterization of ribozymes. 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 key tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Ribozymes: Methods and Protocols seeks to aid scientists in further understanding the catalytically active RNAs .

Introduction.-Characterization of Hammerhead Ribozyme Reactions.-Mechanistic Analysis of the Hepatitis Delta Virus (HDV) Ribozyme: Methods for RNA Preparation, Structure Mapping, Solvent Isotope Effects, and Co-transcriptional Cleavage.-Kinetic Characterization of Hairpin Ribozyme Variants.-Characterization of RNase P RNA Activity.-Group I Intron Ribozymes.-Kinetic Characterization of Group II Intron Folding and Splicing.-Mechanism and Distribution of glmS Ribozymes.-Structure-based Search and in vitro Analysis of Self-cleaving Ribozymes.-Discovery of RNA Motifs using a Computational Pipeline that Allows Insertions in Paired Regions and Filtering of Candidate Sequences.-Crystallographic Analysis of Small Ribozymes and Riboswitches.-Functional Dynamics of RNA Ribozymes Studied by NMR Spectroscopy.-Deoxyribozyme-based, Semisynthetic Access to Stable Peptidyl-tRNAs Exemplified by tRNA^Val Carrying a Macrolide Antibiotic Resistance Peptide.-Probing Functions of the Ribosomal Peptidyl Transferase Center by Nucleotide Analog Interference.-Single Molecule FRET Characterization of Large Ribozyme Folding.-Metal Ion-RNA Interactions Studied via Multinuclear NMR.-Analysis of Catalytic RNA Structure and Function by Nucleotide Analog Interference Mapping.-In Vitro Selection of Metal-Ion-Selective DNAzymes.-In vitro Selection of Allosteric Ribozymes.-Screening Effective Target Sites on mRNA: A Ribozyme Library Approach.-A Computational Approach to Predict Suitable Target Sites for Trans-acting Minimal Hammerhead Ribozymes.-Targeting mRNAs by Engineered Sequence-specific RNase P Ribozymes.-Target Induced SOFA-HDV Ribozyme.-Ribozyme-mediated Trans-insertion-splicing into Target RNAs.-Developing Fluorogenic RNA-cleaving DNAzymes for Biosensing Applications.-Development of Trainable Deoxyribozyme-based Game Playing Automaton.-Rational Design and Tuning of Ribozyme-Based Devices.-In Vivo Screening of Ligand-dependent Hammerhead Ribozymes.-Flexizymes as a tRNA Acylation Tool Facilitating Genetic Code Reprogramming.