Description
Book SynopsisThis 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
Table of Contents1. 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 Mörl, 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. Małecka, Boyang Hua, and Sarah A. Woodson
17. Cotranscriptional RNA Chemical Probing
Courtney E. Szyjka and Eric J. Strobel
