Artificial Riboswitches: Methods and Protocols

ISBN-13: 9781627037549 / Angielski / Twarda / 2014 / 289 str.

Atsushi Ogawa

Opis

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.

Spis treści

1. Computational Design of RNA Libraries for in vitro Selection of Aptamers

Yaroslav Chushak, Jennifer A. Martin, Jorge L. Chávez, Nancy Kelley-Loughnane, and Morley O. Stone

 

2. In vitro Selection of RNA Aptamers for a Small-Molecule Dye

Asako Murata and Shin-ichi Sato

 

3. Development of Photoswitchable RNA Aptamer-Ligand Complexes

Gosuke Hayashi and Kazuhiko Nakatani

 

4. Identification of RNA Aptamers Against Recombinant Proteins with a Hexa-Histidine Tag

Shoji Ohuchi

 

5. Artificial Riboswitch Selection: A FACS-Based Approach

Zohaib Ghazi, Casey C. Fowler, and Yingfu Li

 

6. FRET-Based Optical Assay for Selection of Artificial Riboswitches

Svetlana V. Harbaugh, Molly E. Chapleau, Yaroslav G. Chushak, Morley O. Stone, and Nancy Kelley-Loughnane

 

7. Portable Two-Way Riboswitches: Design and Engineering

Ye Jin and Jian-Dong Huang

 

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, and Jason Micklefield

 

9. Dual Genetic Selection of Synthetic Riboswitches in Escherichia coli

Yoko Nomura and Yohei Yokobayashi

 

10. Nucleotide Kinase-Based Selection System for Genetic Switches

Kohei Ike and Daisuke Umeno

 

11. Measuring Riboswitch Activity in vitro and in Artificial Cells with Purified Transcription-Translation Machinery

Laura Martini and Sheref S. Mansy

 

12. Rational Design of Artificial ON-Riboswitches

Atsushi Ogawa

 

13. Engineering Protein-Responsive mRNA Switch in Mammalian Cells

Kei Endo and Hirohide Saito

 

14. Guanine-Tethered Antisense Oligonucleotides as Synthetic Riboregulators

Masaki Hagihara

 

15. In Vitro Selection of Allosteric Ribozymes that Sense the Bacterial Second Messenger c-di-GMP

Kazuhiro Furukawa, Hongzhou Gu, and Ronald R. Breaker

 

16. Dual-Selection for Evolution of in vivo Functional Aptazymes as Riboswitch Parts

Jonathan A. Goler, James M. Carothers, and Jay D. Keasling

 

17. In vivo Screening for Aptazyme-Based Bacterial Riboswitches

Charlotte Rehm and Jörg S. Hartig

 

18. Engineered Riboswitch as Gene-Regulatory Platform for Reducing Antibiotic Resistance

Libing Liu and Shu Wang

 

19. Construction of Ligand-Responsive microRNAs that Operate Through Inhibition of Drosha Processing

Chase L. Beisel, Ryan J. Bloom, and Christina D. Smolke

 

20. A Three-Dimensional Design Strategy for a Protein-Responsive shRNA Switch

Shunnichi Kashida and Hirohide Saito