RNA Spectroscopy: Methods and Protocols

Front Matter ....Pages i-xi
 Encapsulation of Fluorescently Labeled RNAs into Surface-Tethered Vesicles for Single-Molecule FRET Studies in TIRF Microscopy  (Susann Zelger-Paulus, Mélodie C. A. S. Hadzic, Roland K. O. Sigel, Richard Börner)....Pages 1-16
 Preparation of SNAPf-Beads for Colocalization Single-Molecule Spectroscopy (CoSMoS) of RNA-Protein Complexes  (Reka A. Haraszti, Joerg E. Braun)....Pages 17-22
 Comparative Colocalization Single-Molecule Spectroscopy (CoSMoS) with Multiple RNA Species  (Reka A. Haraszti, Joerg E. Braun)....Pages 23-29
 Dynamic Light Scattering Analysis on RNA Associated to Proteins  (Serena Bernacchi)....Pages 31-39
 Bioinformatic Application of Fluorescence-Based In Vivo RNA Regional Accessibility Data to Identify Novel sRNA Targets  (Emily K. Bowman, Mia K. Mihailovic, Bridget Li, Lydia M. Contreras)....Pages 41-71
 Surface Plasmon Resonance for Investigating Molecular Interactions with RNA  (Carmelo Di Primo)....Pages 73-88
 RNA Folding and Unfolding Under Force: Single-Molecule Experiments and Their Analysis  (Laurent Geffroy, Thierry Bizebard, Ulrich Bockelmann)....Pages 89-100
 Mapping of Posttranscriptional tRNA Modifications by Two-Dimensional Gel Electrophoresis Mass Spectrometry  (Laura Antoine, Philippe Wolff)....Pages 101-110
 Native Electrospray Ionization Mass Spectrometry of RNA-Ligand Complexes  (Philippe Wolff, Eric Ennifar)....Pages 111-118
 Application of FTIR Spectroscopy to Analyze RNA Structure  (Frédéric Geinguenaud, Valeria Militello, Véronique Arluison)....Pages 119-133
 Application of Synchrotron Radiation Circular Dichroism for RNA Structural Analysis  (Etienne Le Brun, Véronique Arluison, Frank Wien)....Pages 135-148
 Application of NIR Raman Spectroscopy to Probe the Flexibility of RNA Structure  (Hui Bon Hoa Gaston)....Pages 149-164
 Small-Angle Neutron Scattering of RNA–Protein Complexes  (Audrone Lapinaite, Teresa Carlomagno, Frank Gabel)....Pages 165-188
 Structural Analysis of RNA by Small-Angle X-ray Scattering  (Anne Théobald-Dietrich, Raphaël de Wijn, Kévin Rollet, Alexandra Bluhm, Joëlle Rudinger-Thirion, Caroline Paulus et al.)....Pages 189-215
 Site-Specific Spin Labeling of RNA for NMR and EPR Structural Studies  (Bertrand Vileno, Isabelle Lebars)....Pages 217-235
 Analysis of the HIV-1 Genomic RNA Dimerization Initiation Site Binding to Aminoglycoside Antibiotics Using Isothermal Titration Calorimetry  (Serena Bernacchi, Eric Ennifar)....Pages 237-250
 Use of Fluorescent Nucleotides to Map RNA-Binding Sites on Protein Surface  (V. Balobanov, N. Lekontseva, A. Mikhaylina, A. Nikulin)....Pages 251-262
 Fluorescent Oligonucleotide Probes for the Quantification of RNA by Real-Time qPCR  (Florent Busi)....Pages 263-280
 Probing RNA–Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical Ultracentrifugation  (Somdeb Mitra, Borries Demeler)....Pages 281-317
 RNA Nanostructure Molecular Imaging  (Olivier Piétrement, Véronique Arluison, Christophe Lavelle)....Pages 319-327
 Grad-cryo-EM: Tool to Isolate Translation Initiation Complexes from Rabbit Reticulocyte Lysate Suitable for Structural Studies  (Javier Rol-Moreno, Lauriane Kuhn, Stefano Marzi, Angelita Simonetti)....Pages 329-339
 Application of NMR Spectroscopy to Determine Small RNA Structure  (Pengzhi Wu, Xiaodan Liu, Qingguo Gong, Yunyu Shi, Jihui Wu)....Pages 341-353
Back Matter ....Pages 355-356