Main description:

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, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, Riboregulator Design and Analysis is an ideal guide for scientists and engineers interested in the design and application of riboregulators and driving further innovation in the field.

Contents:

1. RNP-Based Control Systems for Genetic Circuits in Synthetic Biology Beyond CRISPR

Trevor. R Simmons, Andrew D. Ellington, and Lydia M. Contreras

2. Computational Design of RNA Toehold-Mediated Translation Activators

Kaiyue Wu, Zhaoqing Yan, and Alexander A. Green

3. Design of RNA-Based Translational Repressors

Seongho Hong, Dongwon Park, Soma Chaudhary, Griffin McCutcheon, Alexander A. Green, and Jongmin Kim

4. Design of Ribocomputing Devices for Complex Cellular Logic

Griffin McCutcheon, Soma Chaudhary, Seongho Hong, Dongwon Park, Jongmin Kim, and Alexander A. Green

5. Computational Design of Small Transcription Activating RNAs (STARs)

Baiyang Liu and James Chappell

6. Design and Assembly of Multi-Level Transcriptional and Translational Regulators for Stringent Control of Gene Expression

F. Veronica Greco, Thea Irvine, Claire S. Grierson, and Thomas E. Gorochowski

7. Model-Based Design of Synthetic Antisense RNA for Predictable Gene Repression

Tae Seok Moon

8. Design of a Toolbox of RNA Thermometers

Shaunak Sen, Abhilash Patel, and Krishan Kumar Gola

9. Development of Synthetic Riboswitches to Guide the Evolution of Metabolite Production in Microorganisms

Minsun Kim, Sungho Jang, and Gyoo Yeol Jung

10. Efficient Method to Identify Synthetic Riboswitches Using RNA-Based Capture-SELEX Combined with In Vivo Screening

Janice Kramat and Beatrix Suess

11. RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing

Anna Ender, Peter Stadler, Mario Moerl, and Sven Findeiss

12. Design, Characterization, and Application of Targeted Gene Activation in Bacteria Using a Modular CRISPRa System

Maria Claudia Villegas Kcam and James Chappell

13. Reprogramming TracrRNAs for In Vitro RNA Detection and In Vivo Transcriptional Recording

Chunlei Jiao and Chase L. Beisel

14. Harnessing CRISPR-Cas9 for Epigenetic Engineering

Rosa S. Guerra-Resendez and Isaac B. Hilton

15. RNA Structure Prediction, Analysis, and Design: An Introduction to Web-Based Tools

Raphael Angelo I. Zambrano, Carmen Hernandez-Perez, and Melissa K. Takahashi

16. Single-Molecule FRET Studies of RNA Structural Rearrangements and RNA-RNA Interactions

Ewelina M. Malecka, Boyang Hua, and Sarah A. Woodson

17. Cotranscriptional RNA Chemical Probing

Courtney E. Szyjka and Eric J. Strobel