Riboswitches : methods and protocols / edited by Alexander Serganov.

Contributor(s): Serganov, Alexander
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 540.; Springer protocols (Series): Publisher: New York : Humana, ©2009Description: 1 online resource (xi, 366 pages) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 9781597455589; 159745558XSubject(s): RNA | RNA-protein interactions | Messenger RNA | Ligands (Biochemistry) | RNA -- chemistry | Gene Expression Regulation -- physiology | Laboratory Techniques and Procedures | Ligands (Biochemistry) | Messenger RNA | RNA | RNA-protein interactions | messenger rna | transcriptie | transcription | genen | genes | bacteria | biologische technieken | biological techniques | genregulatie | gene regulation | protocollen | protocols | Molecular Biology (General) | Moleculaire biologie (algemeen)Genre/Form: Laboratory Manual. | Electronic books. Additional physical formats: Print version:: Riboswitches.DDC classification: 572 LOC classification: QP623Online resources: Click here to access online
Contents:
Predicting riboswitch regulation on a genomic scale / Jeffrey E. Barrick -- Enzymatic ligation strategies for the preparation of purine riboswitches with site-specific chemical modification / Renate Rieder, Claudia Höbartner and Ronald Micura -- Application of fluorescent measurements for characterization of riboswitch-ligand interactions / Benoit Heppell [and others] -- Transcriptional approaches to riboswitch studies / Alexander Mironov, Vitaly Epshtein and Evgeny Nudler -- Kinetics of riboswitch regulation studied by in vitro transciption / J. Kenneth Wickiser -- Molecular basis of RNA-mediated gene regulation on the adenine riboswitch by single-molecule approaches / Jean-Franc̜ois Lemay [and others] -- Methods for analysis of ligand-induced RNA confromational changes / Chad A. Brautigam, Catherine A. Wakeman and Wade C. Winkler -- Preparation and crystallization of riboswitch-ligand complexes / Olga Pikovskaya [and others] -- Crystallization of the glmS ribozyme-riboswitch / Daniel J. Klein and Adrian R. Ferré-D'Amaré -- Riboswitch conformations revealed by small-angle X-ray scattering / Jan Lipfert, Daniel Herschlag and Sebastian Doniach -- Time-resolved NMR spectroscopy : ligand-induced refolding of riboswitches / Janina Buck [and others] -- Analysis of the RNA backbone : structural Analysis of riboswitches by in-line probing and selective 2'-hydroxyl acylation and primer extension / Catherine A. Wakeman and Wade C. Winkler -- Identification of metabolite-riboswitch interactions using nucleotide analog interference mapping and suppression / Juliane K. Soukup and Garrett A. Soukup -- RNA-dependent RNA switches in bacteria / Tina M. Henkin -- Probing mRNA structure and sRNA-mRNA interactions in bacteria using enzymes and lead(II) / Clément Chevalier [and others] -- Structural probing of RNA thermosensors / Claude Chiaruttini, Frédéric Allem and Mathias Springer -- Ribosomal initiation complexes probed by toeprinting and effect of trans-acting translational regulators in bacteria / Pierre Fechter [and others] -- Isolation and characterization of the heat shock RNA 1 / Ilya Shamovsky and Evgeny Nudler -- Analysis of tRNA-directed transcription antitermination in the T box system in vivo / Tina M. Henkin -- In vitro selection of conformational probes for riboswitches / Günter Mayer and Michael Famulok -- A green fluorescent protein (GFP)-based plasmid system to study post-transcriptional control of gene expression in vivo / Johannes H. Urban and Jörg Vogel -- High-throughput screens to Discover synthetic riboswitches / Sean A. Lynch, Shana Topp and Justin P. Gallivan -- A mammalian cell-based assay for screening inhibitors of RNA cleavage / Laising Yen, Brent R. Stockwell and Richard C. Mulligan -- In vitro selection of glmS ribozymes / Kristian H. Link and Ronald R. Breaker.
Summary: The revolutionary discoveries of RNA interference and bacterial regulatory RNAs led to further breakthroughs such as the identification 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. In Riboswitches: Methods and Protocols, expert researchers provide comprehensive and up-to-date coverage of various methods used to study riboswitches and other RNAs involved in gene expression control. Examining biochemical and modern biophysical techniques, the volume focuses on mRNAs responding to small organic molecules but expands the definition of a riboswitch to incorporate classes of RNA that undergo conformational transitions in response to other stimuli in order to control the expression of genes. 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Riboswitches: Methods and Protocols promises to inspire both novices and experts working in a wide range of contemporary biological areas who wish to further develop their RNA methodology.
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Includes bibliographical references and index.

Predicting riboswitch regulation on a genomic scale / Jeffrey E. Barrick -- Enzymatic ligation strategies for the preparation of purine riboswitches with site-specific chemical modification / Renate Rieder, Claudia Höbartner and Ronald Micura -- Application of fluorescent measurements for characterization of riboswitch-ligand interactions / Benoit Heppell [and others] -- Transcriptional approaches to riboswitch studies / Alexander Mironov, Vitaly Epshtein and Evgeny Nudler -- Kinetics of riboswitch regulation studied by in vitro transciption / J. Kenneth Wickiser -- Molecular basis of RNA-mediated gene regulation on the adenine riboswitch by single-molecule approaches / Jean-Franc̜ois Lemay [and others] -- Methods for analysis of ligand-induced RNA confromational changes / Chad A. Brautigam, Catherine A. Wakeman and Wade C. Winkler -- Preparation and crystallization of riboswitch-ligand complexes / Olga Pikovskaya [and others] -- Crystallization of the glmS ribozyme-riboswitch / Daniel J. Klein and Adrian R. Ferré-D'Amaré -- Riboswitch conformations revealed by small-angle X-ray scattering / Jan Lipfert, Daniel Herschlag and Sebastian Doniach -- Time-resolved NMR spectroscopy : ligand-induced refolding of riboswitches / Janina Buck [and others] -- Analysis of the RNA backbone : structural Analysis of riboswitches by in-line probing and selective 2'-hydroxyl acylation and primer extension / Catherine A. Wakeman and Wade C. Winkler -- Identification of metabolite-riboswitch interactions using nucleotide analog interference mapping and suppression / Juliane K. Soukup and Garrett A. Soukup -- RNA-dependent RNA switches in bacteria / Tina M. Henkin -- Probing mRNA structure and sRNA-mRNA interactions in bacteria using enzymes and lead(II) / Clément Chevalier [and others] -- Structural probing of RNA thermosensors / Claude Chiaruttini, Frédéric Allem and Mathias Springer -- Ribosomal initiation complexes probed by toeprinting and effect of trans-acting translational regulators in bacteria / Pierre Fechter [and others] -- Isolation and characterization of the heat shock RNA 1 / Ilya Shamovsky and Evgeny Nudler -- Analysis of tRNA-directed transcription antitermination in the T box system in vivo / Tina M. Henkin -- In vitro selection of conformational probes for riboswitches / Günter Mayer and Michael Famulok -- A green fluorescent protein (GFP)-based plasmid system to study post-transcriptional control of gene expression in vivo / Johannes H. Urban and Jörg Vogel -- High-throughput screens to Discover synthetic riboswitches / Sean A. Lynch, Shana Topp and Justin P. Gallivan -- A mammalian cell-based assay for screening inhibitors of RNA cleavage / Laising Yen, Brent R. Stockwell and Richard C. Mulligan -- In vitro selection of glmS ribozymes / Kristian H. Link and Ronald R. Breaker.

Print version record.

The revolutionary discoveries of RNA interference and bacterial regulatory RNAs led to further breakthroughs such as the identification 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. In Riboswitches: Methods and Protocols, expert researchers provide comprehensive and up-to-date coverage of various methods used to study riboswitches and other RNAs involved in gene expression control. Examining biochemical and modern biophysical techniques, the volume focuses on mRNAs responding to small organic molecules but expands the definition of a riboswitch to incorporate classes of RNA that undergo conformational transitions in response to other stimuli in order to control the expression of genes. 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Riboswitches: Methods and Protocols promises to inspire both novices and experts working in a wide range of contemporary biological areas who wish to further develop their RNA methodology.

English.

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