Artificial Riboswitches: Methods and Protocols - Methods in Molecular Biology 2014 edition

Jacket Description/Back: 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. "Table of Contents:1. Computational Design of RNA Libraries for in vitro Selection of AptamersYaroslav Chushak, Jennifer A. Martin, Jorge L. Chavez, Nancy Kelley-Loughnane, and Morley O. Stone 2. In vitro Selection of RNA Aptamers for a Small-Molecule DyeAsako Murata and Shin-ichi Sato 3. Development of Photoswitchable RNA Aptamer-Ligand ComplexesGosuke Hayashi and Kazuhiko Nakatani 4. Identification of RNA Aptamers Against Recombinant Proteins with a Hexa-Histidine TagShoji Ohuchi 5. Artificial Riboswitch Selection: A FACS-Based ApproachZohaib Ghazi, Casey C. Fowler, and Yingfu Li 6. FRET-Based Optical Assay for Selection of Artificial RiboswitchesSvetlana V. Harbaugh, Molly E. Chapleau, Yaroslav G. Chushak, Morley O. Stone, and Nancy Kelley-Loughnane 7. Portable Two-Way Riboswitches: Design and EngineeringYe Jin and Jian-Dong Huang 8. Generation of Orthogonally Selective Bacterial Riboswitches By Targeted Mutagenesis and in vivo ScreeningHelen A. Vincent, Christopher J. Robinson, Ming-Cheng Wu, Neil Dixon, and Jason Micklefield 9. Dual Genetic Selection of Synthetic Riboswitches in Escherichia coliYoko Nomura and Yohei Yokobayashi 10. Nucleotide Kinase-Based Selection System for Genetic SwitchesKohei Ike and Daisuke Umeno 11. Measuring Riboswitch Activity in vitro and in Artificial Cells with Purified Transcription-Translation MachineryLaura Martini and Sheref S. Mansy 12. Rational Design of Artificial ON-RiboswitchesAtsushi Ogawa 13. Engineering Protein-Responsive mRNA Switch in Mammalian CellsKei Endo and Hirohide Saito 14. Guanine-Tethered Antisense Oligonucleotides as Synthetic RiboregulatorsMasaki Hagihara 15. In Vitro Selection of Allosteric Ribozymes that Sense the Bacterial Second Messenger c-di-GMPKazuhiro Furukawa, Hongzhou Gu, and Ronald R. Breaker 16. Dual-Selection for Evolution of in vivo Functional Aptazymes as Riboswitch PartsJonathan A. Goler, James M. Carothers, and Jay D. Keasling 17. In vivo Screening for Aptazyme-Based Bacterial RiboswitchesCharlotte Rehm and Jorg S. Hartig 18. Engineered Riboswitch as Gene-Regulatory Platform for Reducing Antibiotic ResistanceLibing Liu and Shu Wang 19. Construction of Ligand-Responsive microRNAs that Operate Through Inhibition of Drosha ProcessingChase L. Beisel, Ryan J. Bloom, and Christina D. Smolke 20. A Three-Dimensional Design Strategy for a Protein-Responsive shRNA SwitchShunnichi Kashida and Hirohide Saito"Publisher Marketing: Artificial riboswitches and other ligand-responsive gene regulators make it possible to switch protein synthesis ON or OFF with arbitrary ligand molecules. This title focuses on the state-of-the-art methods developed in recent years for creating artificial riboswitches, therefore the volume could be regarded as a collection of recipes for the gene circuit elements in synthetic biology and metabolic engineering.