Structures of Large RNA Molecules and Their Complexes

Part I: RNA Structure and Dynamics

1. Native Purification and Analysis of Long RNAs
Isabel Chillón, Marco Marcia, Michal Legiewicz, Fei Liu, Srinivas Somarowthu and Anna Marie Pyle

2. Characterizing RNA Excited States Using NMR Relaxation Dispersion
Yi Xue, Dawn Kellogg, Isaac J Kimsey, Bharathwaj Sathyamoorthy, Zachary W Stein, Mitchell McBrairty, and Hashim M. Al-Hashimi

3. Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry
Xuesong Shi, Steve Bonilla, Daniel Herschlag and Pehr Harbury

4. 2-Aminopurine Fluorescence as a Probe of Local RNA Structure and Dynamics and Global Folding. Hairpins, Hinges, and Mg2+ ions in a 60 Nucleotide RNA
Michael J Rau and Kathleen B Hall

5. Mod-seq: A High-Throughput Method for Probing RNA Secondary Structure
Yizhu Lin, Gemma E. May, and C. Joel McManus

6. Reproducible Analysis of Sequencing Based RNA Structure Probing Data with User-Friendly Tools.
Lukasz Jan Kielpinski, Nikolaos Sidiropoulos and Jeppe Vinther

7. Computational Methods for RNA Structure Validation and Improvement
Swati Jain, David C. Richardson, and Jane S. Richardson

8. Structures of large RNAs and RNA Protein Complexes Towards Structure Determination of Riboswitches
Jason C. Grigg and Ailong Ke
Part II: RNA-Protein Interactions

9. RRM-RNA Interactions
Tariq Afroz, Zuzana Cienikova, Antoine Cléry and Frédéric H.T-Allain

10. Combining NMR and EPR to Determine Structures of Large RNAs and Protein-RNA Complexes in Solution
Olivier Duss, Maxim Yulikov, Frédéric H.-T. Allain, and Gunnar Jeschke

11. Structural Analysis of Protein-RNA Complexes in Solution Using NMR Paramagnetic Relaxation Enhancements
Janosch Hennig, Lisa R. Warner, Bernd Simon, Arie Geerlof, Cameron D. Mackereth and Michael Sattler

12. Resolving Individual Components in Protein-RNA Complexes Using Small Angle X-Ray Scattering Experiments
Robert P. Rambo

13. Small-Angle Neutron Scattering for Structural Biology of Protein-RNA Complexes
Frank Gabel

14. Studying RNA-Protein Interactions of Pre-mRNA Complexes by Mass Pectrometry
Saadia Qamar, Katharina Kramer, Henning Urlaub

15. RNA Bind-n-Seq: Measuring the Binding Affinity Landscape of RNA Binding Proteins
Nicole J. Lambert, Alex D. Robertson and Christopher B. Burge
Part III: Large RNA-Protein Assemblies

16. Using Molecular Simulation to Model High Resolution Cryo-EM Reconstructions
Serdal 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 Target
Carolin Anders, Ole Niewoehner and Martin Jinek

18. Single-Molecule Pull-down FRET (SiMPull-FRET) to Dissect the Mechanisms of Biomolecular Machines
Matthew L. Kahlscheuer, Julia Widom and Nils G. Walter

19. Single-Molecule Imaging of RNA Splicing in Live Cells
José Rino, Robert M. Martin, Célia Carvalho, Ana C. de Jesus and Maria Carmo-Fonseca