Riboswitches : methods and protocols / edited by Alexander Serganov.

Format:

Book

Contributor:

Serganov, Alexander.

Series:

Methods in molecular biology (Clifton, N.J.) ; v. 540.

Methods in molecular biology, 1064-3745 ; v. 540

Language:

English

Subjects (All):

RNA.

RNA-protein interactions.

Messenger RNA.

Ligands (Biochemistry).

RNA--chemistry.

Gene Expression Regulation--physiology.

Clinical Laboratory Techniques.

Medical Subjects:

RNA--chemistry.

Gene Expression Regulation--physiology.

Clinical Laboratory Techniques.

Genre:

Laboratory manuals.

Physical Description:

xi, 366 pages : illustrations ; 27 cm.

Place of Publication:

New York, NY : Humana, [2009]

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 BiologyTM 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.

Contents:

Predicting riboswitch regulation on a genomic scale / J.E. Barrick

Enzymatic ligation strategies for the preparation of purine riboswitches with site-specific chemical modifications / R. Rieder, C. Höbartner and R. Micura

Application of fluorescent measurements for characterization of riboswitch-ligand interactions / B. Heppell ... [et al.]

Transcriptional approaches to riboswitch studies / A. Mironov, V. Epshtein and E. Nudler

Kinetics of riboswitch regulation studied by in vitro transcription / J.K. Wickiser

Molecular basis of RNA-mediated gene regulation on the adenine riboswitch by single-molecule approaches / J.F. Lemay ... [et al.]

Methods for analysis of ligand-induced RNA conformational changes / C.A. Brautigam, C.A. Wakeman and W.C. Winkler

Monitoring RNA-ligand interactions using isothermal titration calorimetry / S.D. Gilbert and R.T. Batey

Preparation and crystallization of riboswitch-ligand complexes / O. Pikovskaya ... [et al.]

Crystallization of the glmS ribozyme-riboswitch / D.J. Klein and A.R. Ferre-D'Amare

Riboswitch conformations revealed by small-angle X-ray scattering / J. Lipfert, D. Herschlag and S. Doniach

Time-resolved NMR spectroscopy: ligand-induced refolding of riboswitches / J. Buck ... [et al.]

Analysis of the RNA backbone: structural analysis of riboswitches by in-line probing and selective 2'-hydroxyl acylation and primer extension / C.A. Wakeman and W.C. Winkler

Identification of metabolite-riboswitch interactions using nucleotide analog interference mapping and suppression / J.K. Soukup and G.A. Soukup

RNA-dependent RNA switches in bacteria / T.M. Henkin

Probing mRNA structure and sRNA-mRNA interactions in bacteria using enzymes and lead(II) / C. Chevalier ... [et al.]

Structural probing of RNA thermosensors / C. Chiaruttini, F. Allemand, and M. Springer

Ribosomal initiation complexes probed by toeprinting and effect of trans-acting translational regulators in bacteria / P. Fechter ... [et al.]

Isolation and characterization of the heat shock RNA 1 / I. Shamovsky and E. Nudler

Analysis of tRNA-directed transcription antitermination in the T box system in vivo / T.M. Henkin

In vitro selection of conformational probes for riboswitches / G. Mayer and M. Famulok

A green fluorescent protein (GFP)-based plasmid system to study post-transcriptional control of gene expression in vivo / J.H. Urban and J. Vogel

High-throughput screens to discover synthetic riboswitches / S.A. Lynch, S. Topp and J.P. Gallivan

A mammalian cell-based assay for screening inhibitors of RNA cleavage / L. Yen, B.R. Stockwell and R.C. Mulligan

In vitro selection of glmS ribozymes / K.H. Link and R.R. Breaker.

Notes:

"Springer protocols"--Cover.

Includes bibliographical references and index.

ISBN:

1934115886

9781934115886

9781597455589

159745558X

OCLC:

316002776