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This volume looks at the different spectroscopic and biophysical methods used by researchers to study the structure and folding of RNA, and to follow their interactions with proteins. The chapters in this book cover topics such as single-molecule spectroscopy of multiple RNA species; surface plasmon resonance, MS or microcalorimetry for investigating molecular interactions with RNA; FTIR, SAXS, SANS and SRCD spectroscopies to analyze RNA structure; use of fluorescent nucleotides to map RNA-binding sites on proteins surfaces or CryoEM; and much more. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Cutting-edge and comprehensive, RNA Spectroscopy: Methods and Protocols is a valuable resource for anyone interested in learning more about this developing field.
List of contents
Encapsulation of Fluorescently Labelled RNAs into Surface-Tethered Vesicles for Single-Molecule FRET Studies in TIRF Microscopy.- Preparation of SNAPf-Beads for Colocalization Single-Molecule Spectroscopy (CoSMoS) of RNA-Protein Complexes.- Comparative Colocalization Single-Molecule Spectroscopy (CoSMoS) with Multiple RNA Species.- Dynamic Light Scattering Analysis on RNA Associated to Proteins.- Bioinformatic Application of Fluorescence-Based In Vivo RNA Regional Accessibility Data to Identify Novel sRNA Targets.- Surface Plasmon Resonance for Investigating Molecular Interactions with RNA.- RNA folding and Unfolding Under Force: Single-Molecule Experiments and their Analysis.- Mapping of Post-Transcriptional tRNA Modifications by Two-Dimensional Gel Electrophoresis Mass Spectrometry.- Native Electrospray Ionization Mass Spectrometry of RNA-Ligand Complexes.- Application of FTIR Spectroscopy to Analyse RNA Structure.- Application of Synchrotron Radiation Circular Dichroism for RNA Structural Analysis.- Application of NIR Raman Spectroscopy to Probe the Flexibility of RNA Structure.- Small Angle Neutron Scattering of RNA-Protein Complexes.- Structural Analysis of RNA by Small-Angle X-Ray Scattering.- Site-Specific Spin-Labeling of RNA for NMR and EPR Structural Studies.- Analysis of the HIV-1 Genomic RNA Dimerization Initiation Site Binding to Aminoglycoside Antibiotics using Isothermal Titration.- Use of Fluorescent Nucleotides to Map RNA-Binding Sites on Protein Surface.- Fluorescent Oligonucleotide Probes for the Quantification of RNA by Real-Time qPCR.- Probing RNA-Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical Ultracentrifugation.- RNA Nanostructures Molecular Imaging.- Grad-CryoEM: Tool to Isolate Translation Initiation Complexes from Rabbit Reticulocyte Lysate Suitable for Structural Studies.- Application of NMR Spectroscopy to Determine Small RNA Structure.
