Riboswitches

Methods and Protocols

Editors:

ISBN: 978-1-934115-88-6 (Print) 978-1-59745-558-9 (Online)

Table of contents (25 protocols)

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  1. Front Matter

    Pages i-xi

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    Pages 1-13

    Predicting Riboswitch Regulation on a Genomic Scale

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    Pages 15-24

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

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    Pages 25-37

    Application of Fluorescent Measurements for Characterization of Riboswitch–Ligand Interactions

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    Pages 39-51

    Transcriptional Approaches to Riboswitch Studies

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    Pages 53-63

    Kinetics of Riboswitch Regulation Studied By In Vitro Transcription

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    Pages 65-76

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

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    Pages 77-95

    Methods for Analysis of Ligand-Induced RNA Conformational Changes

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    Pages 97-114

    Monitoring RNA–Ligand Interactions Using Isothermal Titration Calorimetry

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    Pages 115-128

    Preparation and Crystallization of Riboswitch–Ligand Complexes

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    Pages 129-139

    Crystallization of the glmS Ribozyme-Riboswitch

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    Pages 141-159

    Riboswitch Conformations Revealed by Small-Angle X-Ray Scattering

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    Pages 161-171

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

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    Pages 173-191

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

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    Pages 193-206

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

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    Pages 207-214

    RNA-Dependent RNA Switches in Bacteria

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    Pages 215-232

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

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    Pages 233-245

    Structural Probing of RNA Thermosensors

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    Pages 247-263

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

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    Pages 265-279

    Isolation and Characterization of the Heat Shock RNA 1

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    Pages 281-290

    Analysis of tRNA-Directed Transcription Antitermination in the T Box System In Vivo

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