Riboregulator Design and Analysis

ISBN-13: 9781071624203 / Angielski / Twarda / 2022

Opis

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.

Spis treści

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 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