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RNA Scaffolds

Methods and Protocols

  • Book
  • © 2015

Overview

Editors:
  1. Luc Ponchon

    1. University of Paris Descartes, Paris, France

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1316)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. A Method to Predict the 3D Structure of an RNA Scaffold

    • Xiaojun Xu, Shi-Jie Chen
    Pages 1-11

  3. Post-crystallization Improvement of RNA Crystal Diffraction Quality

    • Jinwei Zhang, Adrian R. Ferré-D’Amaré
    Pages 13-24

  4. Expression and Purification of RNA–Protein Complexes in Escherichia coli

    • Margueritte El Khouri, Marjorie Catala, Bili Seijo, Johana Chabal, Carine Tisné, Frédéric Dardel et al.
    Pages 25-31

  5. Production of Homogeneous Recombinant RNA Using a tRNA Scaffold and Hammerhead Ribozymes

    • Frank H. T. Nelissen, Hans A. Heus, Sybren S. Wijmenga
    Pages 33-44

  6. In Vivo Production of Small Recombinant RNAs Embedded in a 5S rRNA-Derived Protective Scaffold

    • Victor G. Stepanov, George E. Fox
    Pages 45-65

  7. Detection of RNA–Protein Interactions Using Tethered RNA Affinity Capture

    • Hidekazu Iioka, Ian G. Macara
    Pages 67-73

  8. A Universal Method for Labeling Native RNA in Live Bacterial Cells

    • Irina Smolina, Natalia Broude
    Pages 75-85

  9. Live Cell Imaging Using Riboswitch-Spinach tRNA Fusions as Metabolite-Sensing Fluorescent Biosensors

    • Colleen A. Kellenberger, Zachary F. Hallberg, Ming C. Hammond
    Pages 87-103

  10. RNA Scaffold: Designed to Co-localize Enzymes

    • ZJU_China Team (iGEM 2012), Ming Chen
    Pages 105-112

  11. Artificial Ligase Ribozymes Isolated by a “Design and Selection” Strategy

    • Shigeyoshi Matsumura, Yoshiya Ikawa
    Pages 113-125

  12. Engineering Aptazyme Switches for Conditional Gene Expression in Mammalian Cells Utilizing an In Vivo Screening Approach

    • Charlotte Rehm, Benedikt Klauser, Jörg S. Hartig
    Pages 127-140

  13. Aptazyme-Based Riboswitches and Logic Gates in Mammalian Cells

    • Yoko Nomura, Yohei Yokobayashi
    Pages 141-148

  14. Design and Characterization of Topological Small RNAs

    • Jack Hassall, Paul MacDonald, Teresa Cordero, William Rostain, Alfonso Jaramillo
    Pages 149-167

  15. Folding RNA–Protein Complex into Designed Nanostructures

    • Tomonori Shibata, Yuki Suzuki, Hiroshi Sugiyama, Masayuki Endo, Hirohide Saito
    Pages 169-179

  16. Simple Method for Constructing RNA Triangle, Square, Pentagon by Tuning Interior RNA 3WJ Angle from 60° to 90° or 108°

    • Emil F. Khisamutdinov, My Nguyen Hoan Bui, Daniel Jasinski, Zhengyi Zhao, Zheng Cui, Peixuan Guo
    Pages 181-193

  17. RNA-Mediated CdS-Based Nanostructures

    • Vinit Kumar, Anil Kumar
    Pages 195-210

  18. An Effective Method for Specific Gene Silencing in Escherichia coli Using Artificial Small RNA

    • Geunu Bak, Jee Soo Choi, Wonkyeong Kim, Shinae Suk, Younghoon Lee
    Pages 211-225

  19. Back Matter

    Pages 227-231
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Keywords

About this book

This volume provides techniques on recent developments that use RNA scaffolds as molecular tools. RNA Scaffolds: Methods and Protocols guides readers through methods on various domains as molecular biology, nanotechnologies, and structural biology. Written for the Methods in Molecular Biology series, 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.

Practical and authoritative, RNA Scaffolds: Methods and Protocols will serve as an invaluable reference for those interested in further study into this fascinating field.

Editors and Affiliations

  • University of Paris Descartes, Paris, France

    Luc Ponchon

Bibliographic Information

  • Book Title: RNA Scaffolds

  • Book Subtitle: Methods and Protocols

  • Editors: Luc Ponchon

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-2730-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2015

  • Hardcover ISBN: 978-1-4939-2729-6Published: 13 May 2015

  • Softcover ISBN: 978-1-4939-5589-3Published: 09 October 2016

  • eBook ISBN: 978-1-4939-2730-2Published: 12 May 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 231

  • Number of Illustrations: 20 b/w illustrations, 41 illustrations in colour

  • Topics: Biochemistry, general

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