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  • © 2014

Artificial Riboswitches

Methods and Protocols

Editors:

  • 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 1111)

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-x
  2. Computational Design of RNA Libraries for In Vitro Selection of Aptamers

    • Yaroslav G. Chushak, Jennifer A. Martin, Jorge L. Chávez, Nancy Kelley-Loughnane, Morley O. Stone
    Pages 1-15
  3. In Vitro Selection of RNA Aptamers for a Small-Molecule Dye

    • Asako Murata, Shin-ichi Sato
    Pages 17-28
  4. Development of Photoswitchable RNA Aptamer–Ligand Complexes

    • Gosuke Hayashi, Kazuhiko Nakatani
    Pages 29-40
  5. Artificial Riboswitch Selection: A FACS-Based Approach

    • Zohaib Ghazi, Casey C. Fowler, Yingfu Li
    Pages 57-75
  6. FRET-Based Optical Assay for Selection of Artificial Riboswitches

    • Svetlana V. Harbaugh, Molly E. Chapleau, Yaroslav G. Chushak, Morley O. Stone, Nancy Kelley-Loughnane
    Pages 77-91
  7. Portable Two-Way Riboswitches: Design and Engineering

    • Ye Jin, Jian-Dong Huang
    Pages 93-105
  8. Generation of Orthogonally Selective Bacterial Riboswitches by Targeted Mutagenesis and In Vivo Screening

    • Helen A. Vincent, Christopher J. Robinson, Ming-Cheng Wu, Neil Dixon, Jason Micklefield
    Pages 107-129
  9. Dual Genetic Selection of Synthetic Riboswitches in Escherichia coli

    • Yoko Nomura, Yohei Yokobayashi
    Pages 131-140
  10. Nucleotide Kinase-Based Selection System for Genetic Switches

    • Kohei Ike, Daisuke Umeno
    Pages 141-152
  11. Rational Design of Artificial ON-Riboswitches

    • Atsushi Ogawa
    Pages 165-181
  12. Engineering Protein-Responsive mRNA Switch in Mammalian Cells

    • Kei Endo, Hirohide Saito
    Pages 183-196
  13. In Vitro Selection of Allosteric Ribozymes that Sense the Bacterial Second Messenger c-di-GMP

    • Kazuhiro Furukawa, Hongzhou Gu, Ronald R. Breaker
    Pages 209-220
  14. Dual-Selection for Evolution of In Vivo Functional Aptazymes as Riboswitch Parts

    • Jonathan A. Goler, James M. Carothers, Jay D. Keasling
    Pages 221-235
  15. In Vivo Screening for Aptazyme-Based Bacterial Riboswitches

    • Charlotte Rehm, Jörg S. Hartig
    Pages 237-249
  16. Construction of Ligand-Responsive MicroRNAs that Operate Through Inhibition of Drosha Processing

    • Chase L. Beisel, Ryan J. Bloom, Christina D. Smolke
    Pages 259-267

About this book

Artificial riboswitches and other ligand-responsive gene regulators make it possible to switch protein synthesis ON or OFF with arbitrary ligand molecules. Artificial Riboswitches: Methods and Protocols focuses on the state-of-the-art methods developed in recent years for creating artificial riboswitches, therefore this volume could be regarded as a collection of recipes for the gene circuit elements in synthetic biology and metabolic engineering. Chapters cover topics such as screening or rational design methods for obtaining artificial riboswitches that function in either bacterial or eukaryotic translational systems, protocols for evaluating the activities of the resultant riboswitches, as well as protocols for construction of ligand-dependent, trans-acting gene regulators. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, Artificial Riboswitches: Methods and Protocols seeks to serve not only bioengineers who aim to reprogram cell behaviors and molecular biologists who leverage these regulators for genetic studies, but to all researchers interested in this fascinating field.

Editors and Affiliations

  • Ehime University, Matsuyama, Japan

    Atsushi Ogawa

Bibliographic Information

  • Book Title: Artificial Riboswitches

  • Book Subtitle: Methods and Protocols

  • Editors: Atsushi Ogawa

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-755-6

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2014

  • Hardcover ISBN: 978-1-62703-754-9Published: 21 February 2014

  • Softcover ISBN: 978-1-4939-6330-0Published: 03 September 2016

  • eBook ISBN: 978-1-62703-755-6Published: 18 February 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 289

  • Number of Illustrations: 30 b/w illustrations, 45 illustrations in colour

  • Topics: Biochemistry, general, Biochemical Engineering

Buy it now

Buying options

eBook USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access