Table of Contents

Bioinformatic Discovery of Bacterial Regulatory RNAs using SIPH.-How to Identify CRISPRs in Sequencing Data.-A Strategy for Identifying Non-coding RNAs using Whole-genome Tiling Arrays.-Genetic Screens to Identify Bacterial sRNA Regulators.-Competition Assays Using Barcoded Deletion Strains to Gain Insight Into Small RNA Function.-Use of Semi-quantitative Northern Blot Analysis to Determine Relative Quantities of Bacterial CRISPR Transcripts.-RNA Visualization in Bacteria by Fluorescence in Situ Hybridization.-RNA Structure Prediction: An Overview of Methods.-Crystallization of RNA-Protein Complexes: From Synthesis and Purification of Individual Components to Crystals.-Analysis of RNA Folding and Ligand Binding by Conventional and High-Throughput Calorimetry.-Use of Aptamer Tagging to Identify in vivo Protein Binding Partners of Small Regulatory RNAs.-Gel Mobility Shift Assays to Detect Protein-RNA Interactions.-RNase Footprinting of Protein Binding Sites on an mRNA Target of Small RNAs.-Computational Identification of sRNA Targets.-Detection of sRNA-mRNA Interactions by Electrophoretic Mobility Shift Assay.-Activity of Small RNAs on the Stability of Targeted mRNAs in vivo.-Native Gel Electrophoresis to Study the Binding and Release of RNA Polymerase by 6S RNA.-Ribosome Purification Approaches for Studying Interactions of Regulatory Proteins and RNAs with the Ribosome.-Analysis of Aminoacyl- and Peptidyl-tRNAs by Gel Electrophoresis.- In vitro trans-translation Assays.