Ribozymes

Table of Content

1 Introduction

Eric Westhof

2 Characterization of Hammerhead Ribozyme Reactions

Anne Kalweit, Rita Przybilski, Carsten Seehafer, Marcos de la Peña 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 Müller

5 Characterization of RNase P RNA Activity

Markus Gößringer, 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 Lupták

10 Discovery of RNA Motifs using a Computational Pipeline that Allows Insertions in Paired Regions and Filtering of Candidate Sequences

Randi M. Jimenez, Ladislav Rampásek, Broňa Brejová, Tomás Vinař, Andrej Lupták

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 Fürtig, 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 Predi