Ribozymes: Methods and Protocols

About this book

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 .

Contents

1 Introduction Eric Westhof
2 Characterization of Hammerhead Ribozyme Reactions Anne Kalweit, Rita Przybilski, Carsten Seehafer, Marcos de la Pena and Christian Hammann
3 Mechanistic Analysis of the Hepatitis Delta Virus (HDV) Ribozyme: Methods for RNA Preparation, Structure Mapping, Solvent Isotope Effects, and Co-transcriptional Cleavage Durga M. Chadalavada, Andrea L. Cerrone-Szakal, Jennifer L. Wilcox, Nathan A. Siegfried, and Philip C. Bevilacqua
4 Kinetic Characterization of Hairpin Ribozyme Variants Bettina Appel, Thomas Marschall, Anne Strahland, and Sabine Muller
5 Characterization of RNase P RNA Activity Markus Gossringer, Dominik Helmecke and Roland K. Hartmann
6 Group I Intron Ribozymes HENRIK NIELSEN
7 Kinetic Characterization of Group II Intron Folding and Splicing Olga Fedorova
8 Mechanism and Distribution of glmS Ribozymes Phillip J. McCown, Wade C. Winkler and Ronald R. Breaker
9 Structure-based Search and in vitro Analysis of Self-cleaving Ribozymes Randi M. Jimenez and Andrej Luptak
10 Discovery of RNA Motifs using a Computational Pipeline that Allows Insertions in Paired Regions and Filtering of Candidate Sequences Randi M. Jimenez, Ladislav Rampasek, Brona Brejova, Tomas Vinar, Andrej Luptak
11 Crystallographic Analysis of Small Ribozymes and Riboswitches Geoffrey M. Lippa, Joseph A. Liberman, Jermaine L. Jenkins, Jolanta Krucinska, Mohammad Salim, and Joseph E. Wedekind
12 Functional Dynamics of RNA Ribozymes Studied by NMR Spectroscopy Boris Furtig, Janina Buck, Christian Richter and Harald Schwalbe
13 Deoxyribozyme-based, Semisynthetic Access to Stable Peptidyl-tRNAs Exemplified by tRNAVal Carrying a Macrolide Antibiotic Resistance Peptide Dagmar Graber, Krista Trappl, Jessica Steger, Anna-Skrollan Geiermann, Lukas Rigger, Holger Moroder1, Norbert Polacek and Ronald Micura
14 Probing Functions of the Ribosomal Peptidyl Transferase Center by Nucleotide Analog Interference Matthias D Erlacher, Norbert Polacek
15 Single Molecule FRET Characterization of Large Ribozyme Folding Lucia Cardo, Krishanthi S. Karunatilaka, David Rueda and Roland K. Sigel
16 Metal Ion-RNA Interactions Studied via Multinuclear NMR Daniela Donghi and Roland K. Sigel
17 Analysis of Catalytic RNA Structure and Function by Nucleotide Analog Interference Mapping Soumitra Basu, Mark J. Morris, and Catherine Pazsint
18 In Vitro Selection of Metal-Ion-Selective DNAzymes Hannah E. Ihms and Yi Lu
19 In vitro Selection of Allosteric Ribozymes Nicolas Piganeau
20 Screening Effective Target Sites on mRNA: A Ribozyme Library Approach Hoshang J. Unwalla and John J. Rossi
21 A Computational Approach to Predict Suitable Target Sites for Trans-acting Minimal Hammerhead RibozymesAlberto Mercatanti, Caterina Lande and Lorenzo Citti1
22 Targeting mRNAs by Engineered Sequence-specific RNase P Ribozymes Yong Bai, Naresh Sunkara and Fenyong Liu
23 Target Induced SOFA-HDV Ribozyme Michel V. Levesque and Jean-Pierre Perreault
24 Ribozyme-mediated Trans-insertion-splicing into Target RNAs P. Patrick Dotson II, Jonathan Hart, Christopher Noe, and Stephen M. Testa
25 Developing Fluorogenic RNA-cleaving DNAzymes for Biosensing Applications M. Monsur Ali, Sergio D. Aguirre, Wendy W. K. Mok and Yingfu Li
26 Development of Trainable Deoxyribozyme-based Game Playing Automaton Renjun Pei, Joanne Macdonald, and Milan N. Stojanovic
27 Rational Design and Tuning of Ribozyme-Based Devices Joe C. Liang and Christina D. Smolke
28 In Vivo Screening of Ligand-dependent Hammerhead Ribozymes Athanasios Saragliadis, Benedikt Klauser, and Jorg S. Hartig
29 Flexizymes as a tRNA Acylation Tool Facilitating Genetic Code Reprogramming Yuki Goto and Hiroaki Suga

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