Structures of Large RNA Molecules and Their Complexes

Structures of Large RNA Molecules and Their Complexes

1st Edition - May 22, 2015

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  • Editors: Sarah Woodson, Frédéric Allain
  • Hardcover ISBN: 9780128019344
  • eBook ISBN: 9780128019368

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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.

Key Features

  • Continues the legacy of this premier serial with quality chapters on structures of large RNA molecules and their complexes


Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists.

Table of Contents

  • 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

Product details

  • No. of pages: 654
  • Language: English
  • Copyright: © Academic Press 2015
  • Published: May 22, 2015
  • Imprint: Academic Press
  • Hardcover ISBN: 9780128019344
  • eBook ISBN: 9780128019368

About the Serial Volume Editors

Sarah Woodson

Affiliations and Expertise

Department of Biophysics, Johns Hopkins University, USA

Frédéric Allain

Affiliations and Expertise

Institute of Molecular Biology and Biophysics, ETH Hönggerberg, Switzerland

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