Ribozymes: Methods and Protocols

ISBN-13: 9781493959143 / Angielski / Miękka / 2016 / 480 str.

Jorg S. Hartig

Opis

Ribozymes details protocols and techniques commonly used to study individual ribozymes and their characterizations. Chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and troubleshooting tips.

Spis treści

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 Rampášek, Broňa Brejová, Tomáš 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 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. Lévesque 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 Jörg S. Hartig

 

 

 

 

 

29        Flexizymes as a tRNA Acylation Tool Facilitating Genetic Code Reprogramming

 

Yuki Goto and Hiroaki Suga

 

Blurb

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 .