Structures of Large RNA Molecules and Their Complexes,

Content: Front Cover
 Structures of Large RNA Molecules and Their Complexes
 Copyright
 Contents
 Contributors
 Preface
 Section I: RNA Structure and Dynamics
 Chapter 1: Native Purification and Analysis of Long RNAs
 1. Introduction
 2. Native Purification of Long Noncoding RNAs
 2.1. Construct design
 2.2. DNA plasmid linearization
 2.3. In vitro transcription of RNA
 2.4. DNase digestion
 2.5. Proteinase K treatment
 2.6. EDTA chelation of divalent ions (optional)
 2.7. Buffer exchange and purification
 2.8. Size-exclusion chromatography. 3. Study of the RNA Tertiary Folding by Sedimentation Velocity Analytical Ultracentrifugation3.1. Preparation of samples for a study of RNA folding
 3.2. Assembly of the optical cells, sample loading, and instrument setup
 3.3. Setting up a sedimentation velocity experiment
 3.4. Data analysis
 4. Analysis of the RNA Tertiary Folding by Analytical Size-Exclusion Chromatography
 5. Determination of the Secondary Structure of LncRNAs by Chemical Probing
 5.1. Designing and coupling of primers
 5.2. Generation of sequencing ladders
 5.3. SHAPE reaction
 5.4. DMS reaction. 5.5. Primer extension reaction5.6. Reactions for mobility shift correction
 5.7. Spectral calibration of the instrument
 5.8. Preparation of samples for capillary electrophoresis
 5.9. Data analysis
 5.9.1. Determination of chemical probing reactivity profiles
 5.9.2. Normalization of SHAPE and DMS reactivity profiles
 5.9.3. RNA secondary structure prediction and analysis
 Acknowledgments
 References
 Chapter 2: Characterizing RNA Excited States Using NMR Relaxation Dispersion
 1. Introduction
 2. NMR Relaxation Dispersion
 2.1. Chemical Exchange
 2.2. RD Experiments.