Riboregulator Design and Analysis

This collection explores the latest advances in riboregulators, such as RNA-only systems and ribonucleoprotein systems, and provides detailed techniques to study, evolve, and design them. Beginning with a set of chapters focused on the design and application of small RNA (sRNA) regulator systems, the book continues with sections on techniques to create switchable riboregulator systems known as riboswitches, technologies that leverage RNA-guided CRISPR-Cas systems to edit the epigenome, control gene expression, and create diagnostics, as well as computational and experimental techniques to investigate the sequence-structure-function relationship of RNA systems that can both advance fundamental understanding and rational design of riboregulators. Written for the highly successful 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, andtips on troubleshooting and avoiding known pitfalls. 

RNP-Based Control Systems for Genetic Circuits in Synthetic Biology Beyond CRISPR.- Computational Design of RNA Toehold-Mediated Translation Activators.- Design of RNA-Based Translational Repressors.- Design of Ribocomputing Devices for Complex Cellular Logic.- Computational Design of Small Transcription Activating RNAs (STARs).- Design and Assembly of Multi-Level Transcriptional and Translational Regulators for Stringent Control of Gene Expression.- Model-Based Design of Synthetic Antisense RNA for Predictable Gene Repression.- Design of a Toolbox of RNA Thermometers.- Development of Synthetic Riboswitches to Guide the Evolution of Metabolite Production in Microorganisms.- Efficient Method to Identify Synthetic Riboswitches Using RNA-Based Capture-SELEX Combined with In Vivo Screening.- RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing.- Design, Characterization, and Application of Targeted Gene Activation in Bacteria Using a Modular CRISPRa System.- Reprogramming TracrRNAs for In Vitro RNA Detection and In Vivo Transcriptional Recording.- Harnessing CRISPR-Cas9 for Epigenetic Engineering.- RNA Structure Prediction, Analysis, and Design: An Introduction to Web-Based Tools.- Single-Molecule FRET Studies of RNA Structural Rearrangements and RNA-RNA Interactions.- Cotranscriptional RNA Chemical Probing.