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RNA Structure Determination

Methods and Protocols

  • Book
  • © 2016

Overview

Editors:
  1. Douglas H. Turner

    1. Department of Chemistry and Center for RNA Biology, University of Rochester College of Arts and Sciences, Rochester, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. David H. Mathews

    1. Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1490)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xv
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  2. Crumple: An Efficient Tool to Explore Thoroughly the RNA Folding Landscape

    • Ivan Guerra, Susan J. Schroeder
    Pages 1-14

  3. Secondary Structure Prediction of Single Sequences Using RNAstructure

    • Zhenjiang Zech Xu, David H. Mathews
    Pages 15-34

  4. Prediction of Secondary Structures Conserved in Multiple RNA Sequences

    • Zhenjiang Zech Xu, David H. Mathews
    Pages 35-50

  5. Predicting RNA–RNA Interactions Using RNAstructure

    • Laura DiChiacchio, David H. Mathews
    Pages 51-62

  6. A Method to Predict the Structure and Stability of RNA/RNA Complexes

    • Xiaojun Xu, Shi-Jie Chen
    Pages 63-72

  7. STarMir Tools for Prediction of microRNA Binding Sites

    • Shaveta Kanoria, William Rennie, Chaochun Liu, C. Steven Carmack, Jun Lu, Ye Ding
    Pages 73-82

  8. Traditional Chemical Mapping of RNA Structure In Vitro and In Vivo

    • Pierre Fechter, Delphine Parmentier, ZongFu Wu, Olivier Fuchsbauer, Pascale Romby, Stefano Marzi
    Pages 83-103

  9. High-Throughput Nuclease Probing of RNA Structures Using FragSeq

    • Andrew V. Uzilov, Jason G. Underwood
    Pages 105-134

  10. Mapping RNA Structure In Vitro with SHAPE Chemistry and Next-Generation Sequencing (SHAPE-Seq)

    • Kyle E. Watters, Julius B. Lucks
    Pages 135-162

  11. Experiment-Assisted Secondary Structure Prediction with RNAstructure

    • Zhenjiang Zech Xu, David H. Mathews
    Pages 163-176

  12. RNA Secondary Structure Determination by NMR

    • Jonathan L. Chen, Stanislav Bellaousov, Douglas H. Turner
    Pages 177-186

  13. Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server

    • Joseph D. Yesselman, Rhiju Das
    Pages 187-198

  14. Automated RNA 3D Structure Prediction with RNAComposer

    • Marcin Biesiada, Katarzyna J. Purzycka, Marta Szachniuk, Jacek Blazewicz, Ryszard W. Adamiak
    Pages 199-215

  15. RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS

    • Pawel Piatkowski, Joanna M. Kasprzak, Deepak Kumar, Marcin Magnus, Grzegorz Chojnowski, Janusz M. Bujnicki
    Pages 217-235

  16. Exploring Alternative RNA Structure Sets Using MC-Flashfold and db2cm

    • Paul Dallaire, François Major
    Pages 237-251

  17. NMR Methods for Characterization of RNA Secondary Structure

    • Scott D. Kennedy
    Pages 253-264

  18. The Quick and the Dead: A Guide to Fast Phasing of Small Ribozyme and Riboswitch Crystal Structures

    • Jermaine L. Jenkins, Joseph E. Wedekind
    Pages 265-280

  19. Back Matter

    Pages 281-283
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Keywords

About this book

This volume provides protocols and procedures for determining and modeling RNA structure.  Chapters guide the reader through protocols for RNA secondary structure prediction, single sequence modeling, Crumple,  RNAstructure to model conserved secondary structures with multiple homologs,  the prediction of bimolecular secondary structures with RNAstructure, STarMir, protocols for structure mapping, mapping data to constrain or restrain RNA secondary structure prediction with RNAstructure, unassigned NMR resonances, modeling protocols for Rosetta FARFAR, RNAComposer , ModeRNA, and MC-Fold. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and Practical, RNA Structure Determination:Methods and Protocols aims to ensure successful results in the further study of this vital field.

Editors and Affiliations

  • Department of Chemistry and Center for RNA Biology, University of Rochester College of Arts and Sciences, Rochester, USA

    Douglas H. Turner

  • Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, USA

    David H. Mathews

Bibliographic Information

  • Book Title: RNA Structure Determination

  • Book Subtitle: Methods and Protocols

  • Editors: Douglas H. Turner, David H. Mathews

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-6433-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2016

  • Hardcover ISBN: 978-1-4939-6431-4Published: 24 September 2016

  • Softcover ISBN: 978-1-4939-8198-4Published: 27 June 2018

  • eBook ISBN: 978-1-4939-6433-8Published: 24 September 2016

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XV, 283

  • Number of Illustrations: 15 b/w illustrations, 66 illustrations in colour

  • Topics: Human Genetics

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