Cell-Free Gene Expression: Methods and Protocols

ISBN-13: 9781071620007 / Angielski / Miękka / 2023 / 435 str.

Ashty S. Karim; Michael C. Jewett

Opis

This detailed volume explores perspectives and methods using cell-free expression (CFE) to enable next-generation synthetic biology applications. The first section focuses on tools for CFE systems, including a primer on DNA handling and reproducibility, as well as methods for cell extract preparation from diverse organisms and enabling high-throughput cell-free experimentation. The second section provides an array of applications for CFE systems, such as metabolic engineering, membrane-based and encapsulated CFE, cell-free sensing and detection, and educational kits. 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, Cell‐Free Gene Expression: Methods and Protocols serves as an ideal guide for researchers seeking technical methods to current aspects of CFE and related applications.

Spis treści

Part I: Tools for Cell-Free Expression Systems

 

1. Best Practices for DNA Template Preparation towards Improved Reproducibility in Cell-Free Protein Production

            Eugenia F. Romantseva, Drew S. Tack, Nina Alperovich, David Ross, and Elizabeth A. Strychalski

 

2. Simple Extract Preparation Methods for E. coli-Based Cell-Free Expression

            Alissa C. Mullin, Taylor Slouka, and Javin P. Oza

 

3. Preparation and Screening of Cell-Free Extract from Non-Growing Escherichia coli A19 Cells

            Florian Hiering, Jurek Failmezger, and Martin Siemann-Herzberg

 

4. Cell-Free Protein Synthesis Using Pichia pastoris

            Alex J. Spice, Rochelle Aw, and Karen M. Polizzi

 

5. A Streptomyces-Based Cell-Free Protein Synthesis System for High-Level Protein Expression

            Huiling Xu, Wan-Qiu Liu, and Jian Li

 

6. In Vitro Reconstitution Platforms of Mammalian Cell-Free Expressed Membrane Proteins

            Hossein Moghimianavval, Yen-Yu Hsu, Alessandro Groaz, and Allen P. Liu

 

7. High-Throughput Experimentation Using Cell-Free Protein Synthesis Systems

            Conary Meyer, Chuqing Zhou, Zecong Fang, Marjorie L. Longo, Tingrui Pan, and Cheemeng Tan

 

8. Cell-Free Gene Expression from DNA Brushes

            Michael Levy, Ohad Vonshak, Yiftach Divon, Ferdinand Greiss, Noa Avidan, Shirley S. Daube, and Roy H. Bar-Ziv

 

9. Efficient and Precise Protein Synthesis in a Cell-Free System Using a Set of In Vitro Transcribed tRNAs with Nucleotide Modifications

            Kazuaki Amikura, Keita Hibi, and Yoshihiro Shimizu

 

10. Measurement of Transcription, Translation, and Other Enzymatic Processes during Cell-Free Expression Using PERSIA

            Scott Wick and Peter A. Carr

 

Part II: Applications of Cell-Free Expression Systems

 

11. Cell-Free Noncanonical Redox Cofactor Systems

            William B. Black and Han Li

 

12. Cell-Free Protein Synthesis for High-Throughput Biosynthetic Pathway Prototyping

            Blake J. Rasor, Bastian Vögeli, Michael C. Jewett, and Ashty S. Karim

 

13. Metabolomics Analysis of Cell-Free Expression Systems Using Gas Chromatography-Mass Spectrometry

            April M. Miguez, Yan Zhang, and Mark P. Styczynski

 

14. Liposome Preparation by 3D-Printed Microcapillary-Based Apparatus

            Orion M. Venero, Wakana Sato, Joseph M. Heili, Christopher Deich, and Katarzyna P. Adamala

 

15. Microfluidic Production of Porous Polymer Cell-Mimics Capable of Gene Expression

            Imre Banlaki, François-Xavier Lehr, and Henrike Niederholtmeyer

 

16. Cell-Free Membrane Protein Expression into Hybrid Lipid/Polymer Vesicles

            Miranda L. Jacobs and Neha P. Kamat

 

17. Cell-Free Synthesis Strategies to Probe Co-Translational Folding of Proteins within Lipid Membranes

            Nicola J. Harris, Eamonn Reading, and Paula J. Booth

 

18. Assembly of RNA Nanostructures from Double Crossover Tiles

            Jaimie Marie Stewart, Hari K.K. Subramanian, and Elisa Franco

 

19. Cell-Free Biosensors and AI Integration

            Paul Soudier, Léon Faure, Maish Kushwaha, and Jean-Loup Faulon

 

20. ROSALIND: Rapid Detection of Chemical Contaminants with In Vitro Transcription Factor-Based Biosensors

            Jaeyoung K. Jung, Khalid K. Alam, and Julius B. Lucks

 

21. Optical Sensing in Cell-Free Expression

            Junzhu Yang and Yuan Lu

 

22. Cell-Free Paper-Based Analysis of Gut Microbiota and Host Biomarkers

            Melissa K. Takahashi, Xiao Tan, and Aaron J. Dy

 

23. Detection of Norovirus Using Paper-Based Cell-Free Systems

            Kaiyue Wu and Alexander A. Green

 

24. A TXTL-Based Assay to Rapidly Identify PAMs for CRISPR-Cas Systems with Multi-Protein Effector Complexes

            Franziska Wimmer, Frank Englert, and Chase L. Beisel

 

25. Implementing Hands-On Molecular and Synthetic Biology Education Using Cell-Free Technology

            Ally Huang, Bruce Bryan, Sebastian Kraves, Ezequiel Alvarez-Saavedra, and Jessica C. Stark