Structures of Large RNA Molecules and Their Complexes

Part I: RNA Structure and Dynamics1. Native Purification and Analysis of Long RNAsIsabel Chillón, Marco Marcia, Michal Legiewicz, Fei Liu, Srinivas Somarowthu and Anna Marie Pyle2. Characterizing RNA Excited States Using NMR Relaxation DispersionYi Xue, Dawn Kellogg, Isaac J Kimsey, Bharathwaj Sathyamoorthy, Zachary W Stein, Mitchell McBrairty, and Hashim M. Al-Hashimi3. Quantifying Nucleic Acid Ensembles with X-ray Scattering InterferometryXuesong Shi, Steve Bonilla, Daniel Herschlag and Pehr Harbury4. 2-Aminopurine Fluorescence as a Probe of Local RNA Structure and Dynamics and Global Folding. Hairpins, Hinges, and Mg2+ ions in a 60 Nucleotide RNAMichael J Rau and Kathleen B Hall5. Mod-seq: A High-Throughput Method for Probing RNA Secondary StructureYizhu Lin, Gemma E. May, and C. Joel McManus6. Reproducible Analysis of Sequencing Based RNA Structure Probing Data with User-Friendly Tools.Lukasz Jan Kielpinski, Nikolaos Sidiropoulos and Jeppe Vinther7. Computational Methods for RNA Structure Validation and ImprovementSwati Jain, David C. Richardson, and Jane S. Richardson8. Structures of large RNAs and RNA Protein Complexes Towards Structure Determination of RiboswitchesJason C. Grigg and Ailong KePart II: RNA-Protein Interactions9. RRM-RNA InteractionsTariq Afroz, Zuzana Cienikova, Antoine Cléry and Frédéric H.T-Allain10. Combining NMR and EPR to Determine Structures of Large RNAs and Protein-RNA Complexes in SolutionOlivier Duss, Maxim Yulikov, Frédéric H.-T. Allain, and Gunnar Jeschke11. Structural Analysis of Protein-RNA Complexes in Solution Using NMR Paramagnetic Relaxation EnhancementsJanosch Hennig, Lisa R. Warner, Bernd Simon, Arie Geerlof, Cameron D. Mackereth and Michael Sattler12. Resolving Individual Components in Protein-RNA Complexes Using Small Angle X-Ray Scattering ExperimentsRobert P. Rambo13. Small-Angle Neutron Scattering for Structural Biology of Protein-RNA Complexes Frank Gabel14. Studying RNA-Protein Interactions of Pre-mRNA Complexes by Mass PectrometrySaadia Qamar, Katharina Kramer, Henning Urlaub15. RNA Bind-n-Seq: Measuring the Binding Affinity Landscape of RNA Binding Proteins Nicole J. Lambert, Alex D. Robertson and Christopher B. BurgePart III: Large RNA-Protein Assemblies16. Using Molecular Simulation to Model High Resolution Cryo-EM ReconstructionsSerdal Kirmizialtin, Justus Loerke, Elmar Behrmann, Christian M. T. Spahn, and Karissa Y. Sanbonmatsu 17. In Vitro Reconstitution and Crystallization of Cas9 Endonuclease Bound to a Guide RNA and a DNA TargetCarolin Anders, Ole Niewoehner and Martin Jinek18. Single-Molecule Pull-down FRET (SiMPull-FRET) to Dissect the Mechanisms of Biomolecular MachinesMatthew L. Kahlscheuer, Julia Widom and Nils G. Walter19. Single-Molecule Imaging of RNA Splicing in Live CellsJosé Rino, Robert M. Martin, Célia Carvalho, Ana C. de Jesus and Maria Carmo-Fonseca