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Riboswitches

Methods and Protocols

  • Book
  • © 2009

Overview

Editors:
  1. Alexander Serganov
    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • A comprehensive and timely reference volume for basic and applied research on regulatory RNAs
  • Covers a wide range of assay formats and systems from the computerized prediction of regulatory RNA elements to their detailed structure-function characterization
  • Focuses on both natural and synthetic RNA molecules
  • Provides step-by-step protocols of rigorously tested classical and cutting-edge in vivo and in vitro methods
  • Presents techniques easily adaptable for experiments with any RNA species
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 540)

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Table of contents (25 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Predicting Riboswitch Regulation on a Genomic Scale

    • Jeffrey E. Barrick
    Pages 1-13

  3. Enzymatic Ligation Strategies for the Preparation of Purine Riboswitches with Site-Specific Chemical Modifications

    • Renate Rieder, Claudia Höbartner, Ronald Micura
    Pages 15-24

  4. Application of Fluorescent Measurements for Characterization of Riboswitch–Ligand Interactions

    • Benoit Heppell, Jérôme Mulhbacher, J. Carlos Penedo, Daniel A. Lafontaine
    Pages 25-37

  5. Transcriptional Approaches to Riboswitch Studies

    • Alexander Mironov, Vitaly Epshtein, Evgeny Nudler
    Pages 39-51

  6. Kinetics of Riboswitch Regulation Studied By In Vitro Transcription

    • J. Kenneth Wickiser
    Pages 53-63

  7. Molecular Basis of RNA-Mediated Gene Regulation on the Adenine Riboswitch by Single-Molecule Approaches

    • Jean-François Lemay, J. Carlos Penedo, Jérôme Mulhbacher, Daniel A. Lafontaine
    Pages 65-76

  8. Methods for Analysis of Ligand-Induced RNA Conformational Changes

    • Chad A. Brautigam, Catherine A. Wakeman, Wade C. Winkler
    Pages 77-95

  9. Monitoring RNA–Ligand Interactions Using Isothermal Titration Calorimetry

    • Sunny D. Gilbert, Robert T. Batey
    Pages 97-114

  10. Preparation and Crystallization of Riboswitch–Ligand Complexes

    • Olga Pikovskaya, Artem A. Serganov, Ann Polonskaia, Alexander Serganov, Dinshaw J. Patel
    Pages 115-128

  11. Crystallization of the glmS Ribozyme-Riboswitch

    • Daniel J. Klein, Adrian R. Ferré-D’Amaré
    Pages 129-139

  12. Riboswitch Conformations Revealed by Small-Angle X-Ray Scattering

    • Jan Lipfert, Daniel Herschlag, Sebastian Doniach
    Pages 141-159

  13. Time-Resolved NMR Spectroscopy: Ligand-Induced Refolding of Riboswitches

    • Janina Buck, Boris Fürtig, Jonas Noeske, Jens Wöhnert, Harald Schwalbe
    Pages 161-171

  14. Analysis of the RNA Backbone: Structural Analysis of Riboswitches by In-Line Probing and Selective 2’-Hydroxyl Acylation and Primer Extension

    • Catherine A. Wakeman, Wade C. Winkler
    Pages 173-191

  15. Identification of Metabolite–Riboswitch Interactions Using Nucleotide Analog Interference Mapping and Suppression

    • Juliane K. Soukup, Garrett A. Soukup
    Pages 193-206

  16. RNA-Dependent RNA Switches in Bacteria

    • Tina M. Henkin
    Pages 207-214

  17. Probing mRNA Structure and sRNA–mRNA Interactions in Bacteria Using Enzymes and Lead(II)

    • Clément Chevalier, Thomas Geissmann, Anne-Catherine Helfer, Pascale Romby
    Pages 215-232

  18. Structural Probing of RNA Thermosensors

    • Claude Chiaruttini, Frédéric Allem, Mathias Springer
    Pages 233-245

  19. Ribosomal Initiation Complexes Probed by Toeprinting and Effect of trans-Acting Translational Regulators in Bacteria

    • Pierre Fechter, Clément Chevalier, Gulnara Yusupova, Marat Yusupov, Pascale Romby, Stefano Marzi
    Pages 247-263

  20. Isolation and Characterization of the Heat Shock RNA 1

    • Ilya Shamovsky, Evgeny Nudler
    Pages 265-279
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Keywords

About this book

The transfer of hereditary information from genes to proteins is one of the essential pr- esses in all living organisms on our planet. Some genes are expressed without modu- tion throughout the life of a cell, while many others require various degrees of control to precisely balance cellular metabolism with environmental conditions. For many years, researchers attributed this regulatory function to protein molecules, which can direct gene expression at multiple levels, in response to various input signals, and with different degrees of selectivity. Even when the control of gene expression was achieved via direct interactions between proteins and mRNAs, the active role was routinely assigned to p- teins, while RNAs were considered merely as recipient molecules. The discovery of RNA interference and multiple bacterial regulatory RNAs caused a shift from the perception of proteins as the predominant regulators of gene expression to the acknowledgement of the importance of RNAs in many regulatory circuits. Such a viewpoint received strong support several years ago after the discovery of riboswitches and related RNA sensors – mRNA regions capable of alternating their conformations in response to the presence of cellular metabolites and other physical or chemical cues. These classes of RNA pass on cellular and environmental information directly to transcription or translation machinery without the assistance of proteins. The riboswitches are commonly defined as evolutionarily conserved mRNA regions capable of specific binding to metabolite molecules, and, as a result, adopting a particular RNA conformation that modulates gene expression.

Reviews

From the reviews:

"Riboswitches are among the latest additions to the growing field of RNA-based gene expression control systems found in both prokaryotic and eukaryotic cells. … useful in various aspects of work on riboswitches and other regulatory RNAs. … It also refers to pertinent and up-to-date literature. … The reviewed book can be strongly recommended to RNA researchers with different levels of expertise, as well as to those who learn or teach in this field." (Joanna Ciesla, Acta Biochimica Polonica, Vol. 56 (3), 2009)

“This book is a good collection of ‘Methods and Protocols’ for studying … riboswitches as well as some other RNAs involved in gene expression. … Readers are introduced to a broad range of RNA methodologies from basic to applied in this book. I … recommend the book for researchers who work in the area of riboswitches, but also for other scientists who are involved in RNA-relevant studies.” (Atsushi Ogawa, ChemBioChem, Vol. 10, 2009)

Bibliographic Information

  • Book Title: Riboswitches

  • Book Subtitle: Methods and Protocols

  • Editors: Alexander Serganov

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-59745-558-9

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2009

  • Hardcover ISBN: 978-1-934115-88-6Published: 17 April 2009

  • Softcover ISBN: 978-1-61737-947-5Published: 19 November 2010

  • eBook ISBN: 978-1-59745-558-9Published: 21 April 2009

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 366

  • Number of Illustrations: 65 b/w illustrations

  • Topics: Biochemistry, general, Nucleic Acid Chemistry, Gene Expression

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