Ogawa A. (Ed.) Artificial Riboswitches. Methods and Protocols

Humana Press, 2014 — 289p. — (Methods in Molecular Biology 1111) — ISBN: 978-1-62703-755-6 (eBook), 978-1-62703-754-9 (Hardcover).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.Computational Design of RNA Libraries for In Vitro Selection of Aptamers
In Vitro Selection of RNA Aptamers for a Small-Molecule Dye
Development of Photoswitchable RNA Aptamer–Ligand Complexes
Identification of RNA Aptamers Against Recombinant Proteins with a Hexa-Histidine Tag
Artificial Riboswitch Selection: A FACS-Based Approach
FRET-Based Optical Assay for Selection of Artificial Riboswitches
Portable Two-Way Riboswitches: Design and Engineering
Generation of Orthogonally Selective Bacterial Riboswitches by Targeted Mutagenesis and In Vivo Screening
Dual Genetic Selection of Synthetic Riboswitches in Escherichia coli
Nucleotide Kinase-Based Selection System for Genetic Switches
Measuring Riboswitch Activity In Vitro and in Artificial Cells with Purified Transcription–Translation Machinery
Rational Design of Artificial ON-Riboswitches
Engineering Protein-Responsive mRNA Switch in Mammalian Cells
Guanine-Tethered Antisense Oligonucleotides as Synthetic Riboregulators
In Vitro Selection of Allosteric Ribozymes that Sense the Bacterial Second Messenger c-di-GMP
Dual-Selection for Evolution of In Vivo Functional Aptazymes as Riboswitch Parts
In Vivo Screening for Aptazyme-Based Bacterial Riboswitches
Engineered Riboswitch as a Gene-Regulatory Platform for Reducing Antibiotic Resistance
Construction of Ligand-Responsive MicroRNAs that Operate Through Inhibition of Drosha Processing
A Three-Dimensional Design Strategy for a Protein-Responsive shRNA Switch