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Riboswitches : methods and protocols / edited by Alexander Serganov. — New York, NY : Humana, c2009. – (58.17/M592/v.540) |
Contents
Contents
1 Predicting Riboswitch Regulation on a Genomic Scale
2 Enzymatic Ligation Strategies for the Preparation of Purine Riboswitches with Site-Specific Chemical Modifications 15
3 Application of Fluorescent Measurements for Characterization of Riboswitch-Ligand Interactions 25
4 Transcriptional Approaches to Riboswitch Studies
5 Kinetics of Riboswitch Regulation Studied By In Vitro Transcription 53
6 Molecular Basis of RNA-Mediated Gene Regulation on the Adenine Riboswitch by Single-Molecule Approaches 65
7 Methods for Analysis of Ligand-Induced RNA Conformational Changes 77
8 Monitoring RNA-Ligand Interactions Using Isothermal Titration Calorimetry 97
9 Preparation and Crystallization of Riboswitch-Ligand Complexes 115
10 Crystallization of the glmS Ribozyme-Riboswitch 129
11 Riboswitch Conformations Revealed by Small-Angle X-Ray Scattering 141
12 Time-Resolved NMR Spectroscopy: Ligand-Induced Refolding of Riboswitches 161
13 Analysis of the RNA Backbone: Structural Analysis of Riboswitches by In-Line Probing and Selective 2"-Hydroxyl Acylation and Primer Extension (SHAPE) 173
14 Identification of Metabolite-Riboswitch Interactions Using Nucleotide Analog Interference Mapping and Suppression 193
15 RNA-Dependent RNA Switches in Bacteria 207
16 Probing mRNA Structure and sRNA-mRNA Interactions in Bacteria Using Enzymes and Lead(II)
17 Structural Probing of RNA Thermosensors 233
18 Ribosomal Initiation Complexes Probed by Toeprinting and Effect of trans-Acting Translational Regulators in Bacteria
19 Isolation and Characterization of the Heat Shock RNA 1 (HSR1) 265
20 Analysis of tRNA-Directed Transcription Antitermination in the T Box System in vivo
21 In vitro Selection of Conformational Probes for Riboswitches
22 A Green Fluorescent Protein (GFP) Based Plasmid System to Study Post-Transcriptional Control of Gene Expression In Vivo 301
23 High-Throughput Screens to Discover Synthetic Riboswitches 321
24 A Mammalian Cell-Based Assay for Screening Inhibitors of RNA Cleavage
25 In Vitro Selection of glmS Ribozymes
Index
