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This volume provides a wide spectrum of multidisciplinary approaches for studying RNA structure and dynamics, including detailed accounts of experimental and computational procedures. Chapters guide readers through cryo-electron microscopy, crystallography, isothermal titration calorimetry, small angle X-ray scattering, single-molecule Förster Energy transfer, X-ray free electron laser, atomic force microscopy, computational simulation, and prediction. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.
Authoritative and cutting-edge, RNA Structure and Dynamics aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.
List of contents
Co-transcriptional Assembly and Native Purification of Large RNA-RNA Complexes for Structural Analyses.- Probing RNA Structures and Interactions using Fluorescence Lifetime Analyses.- Characterizing Fluorescence Properties of Turn-on RNA Aptamers.- Probing Transient Riboswitch Structures via Single Molecule Accessibility Analysis.- Isothermal Titration Calorimetry Analysis of a Cooperative Riboswitch using an Interdependent-Sites Binding Model.- Application of Molecular Dynamics to Expand Docking Program's Exploratory Capabilities and to Evaluate Its Predictions.- Exploring the Binding Process of Cognate Ligand to add Adenine Riboswitch Aptamer by using Explicit Solvent Molecular Dynamics (MD) Simulation.- Prediction of Dynamic RBP-RNA Interactions using PrismNet.- High-resolution Atomic Force Microscopy Imaging of RNA molecules in solution.- 3D Structural Analysis of Long Non-coding RNA by Small Angle X-ray Scattering and Computational Modeling.- Combining Biophysical Methods for Structure-function Analyses of RNA in Solution.- Near-Atomic Resolution Cryo-EM Image Reconstruction of RNA.- Auto-DRRAFTER: Automated RNA Modeling Based on Cryo-EM Density.- X-ray Crystallography to Study Conformational Changes in a TPP Riboswitch.- Preparation of RNA Microcrystals for Serial Femtosecond Crystallography Experiments.- Mix-and-Inject Serial Femtosecond Crystallography to Capture RNA Riboswitch Intermediates.
