Main description:

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 (TM) 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:

Ribozymes

Table of Content

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 Goessringer, 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 Joerg S. Hartig

29 Flexizymes as a tRNA Acylation Tool Facilitating Genetic Code Reprogramming

Yuki Goto and Hiroaki Suga