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.
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.
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
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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