Structures of Large RNA Molecules and Their Complexes, Vol 558. Methods in Enzymology

  • ID: 3103090
  • Book
  • 654 Pages
  • Elsevier Science and Technology
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This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in RNA folding and dynamics, RNA-protein interactions and large RNPs.
  • Continues the legacy of this premier serial with quality chapters on structures of large RNA molecules and their complexes
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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
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