RNA Structure and Dynamics

ISBN-13: 9781071626863 / Angielski / Twarda / 2022

Opis

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.  

Spis treści

1               Co-transcriptional Assembly and Native Purification of Large RNA-RNA Complexes for Structural Analyses

Krishna P. Sapkota, Shuang Li, and Jinwei Zhang

2               Probing RNA Structures and Interactions using Fluorescence Lifetime Analyses

Charles Bou-Nader and Jinwei Zhang

3               Characterizing Fluorescence Properties of Turn-on RNA Aptamers

Robert J. Trachman III, Katie A. Link, Jay R. Knutson, and Adrian R. Ferré-D’Amaré

4               Probing Transient Riboswitch Structures via Single Molecule Accessibility Analysis

Robb Welty, Andreas Schmidt, and Nils G. Walter

5               Isothermal Titration Calorimetry Analysis of a Cooperative Riboswitch using an Interdependent-Sites Binding Model

Chapin E. Cavender, Griffin M. Schroeder, David H. Mathews, and Joseph E. Wedekind

6               Application of Molecular Dynamics to Expand Docking Program’s Exploratory Capabilities and to Evaluate Its Predictions

Wojciech K. Kasprzak and Bruce A. Shapiro

7               Exploring the Binding Process of Cognate Ligand to add Adenine Riboswitch Aptamer by using Explicit Solvent Molecular Dynamics (MD) Simulation

Lei Bao and Yi Xiao

8               Prediction of Dynamic RBP-RNA Interactions using PrismNet

Wenze Huang and Qiangfeng Cliff Zhang

9               High-resolution Atomic Force Microscopy Imaging of RNA molecules in solution

Jienyu Ding

10           3D Structural Analysis of Long Non-coding RNA by Small Angle X-ray Scattering and Computational Modeling

Jie Zhang, Binxian Chen, and Xianyang Fang

11           Combining Biophysical Methods for Structure-function Analyses of RNA in Solution

Yun-Tzai Lee, Lixin Fan, Jienyu Ding, and Yun-Xing Wang

12           Near-Atomic Resolution Cryo-EM Image Reconstruction of RNA

Shanshan Li, Kaiming Zhang, and Wah Chiu

13           Auto-DRRAFTER: Automated RNA Modeling Based on Cryo-EM Density

Haiyun Ma, Phillip Pham, Bingnan Luo, Ramya Rangan, Kalli Kappel, Zhaoming Su, and Rhiju Das

14           X-ray Crystallography to Study Conformational Changes in a TPP Riboswitch

Ashok Nuthanakanti, Ascensión Ariza-Mateos, and Alexander Serganov

15           Preparation of RNA Microcrystals for Serial Femtosecond Crystallography Experiments

Jason R. Stagno

16           Mix-and-Inject Serial Femtosecond Crystallography to Capture RNA Riboswitch Intermediates

Jason R. Stagno, Juraj Knoska, Henry N. Chapman, and Yun-Xing Wang