ArticleProceedings of the National Academy of Sciences of the United States of America2019
Cell-free gene-regulatory network engineering with synthetic transcription factors.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Automated synthetic cell-based screening for designed proteins with emergent functions.Nature communications · 2026Article
- A T7 RNAP regulatory toolbox for cell-free network engineering and biosensing applications.Nature communications · 2026Article
- Advances in natural product discovery: strategies, technologies, and insights.Natural products and bioprospecting · 2026Review
- Online monitoring of the mitochondrial respiration activity and protein formation in the Almost Living Cell-free Expression (ALiCE) system.BMC biotechnology · 2025Article
- Cell-Free Gene Expression: Methods and Applications.Chemical reviews · 2025Review
- Regulatory Components for Bacterial Cell-Free Systems Engineering.ACS synthetic biology · 2024Review
- Plug-and-play protein biosensors using aptamer-regulated in vitro transcription.Nature communications · 2024Article
- Applications of cell free protein synthesis in protein design.Protein science : a publication of the Protein Society · 2024Review
- On biochemical constructors and synthetic cells.Interface focus · 2023Article
- Engineering activatable promoters for scalable and multi-input CRISPRa/i circuits.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Context-Aware Technology Mapping in Genetic Design Automation.ACS synthetic biology · 2023Article
- Bottom-Up Synthetic Biology Using Cell-Free Protein Synthesis.Advances in biochemical engineering/biotechnology · 2023Review
- Cell-Free Production Systems in Droplet Microfluidics.Advances in biochemical engineering/biotechnology · 2023Review
- Characterizing a New Fluorescent Protein for a Low Limit of Detection Sensing in the Cell-Free System.ACS synthetic biology · 2022Article
- A versatile active learning workflow for optimization of genetic and metabolic networks.Nature communications · 2022Article
- A microfluidic optimal experimental design platform for forward design of cell-free genetic networks.Nature communications · 2022Article
- Biochemistry of Aminoacyl tRNA Synthetase and tRNAs and Their Engineering for Cell-Free and Synthetic Cell Applications.Frontiers in bioengineering and biotechnology · 2022Review
- Molecular profile reveals immune-associated markers of medulloblastoma for different subtypes.Frontiers in immunology · 2022Article
- Transcription factor-based biosensors: a molecular-guided approach for natural product engineering.Current opinion in biotechnology · 2021Review
- Synthetic Biology towards Improved Flavonoid Pharmacokinetics.Biomolecules · 2021Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene-regulatory networks are ubiquitous in nature and critical for bottom-up engineering of synthetic networks. Transcriptional repression is a fundamental function that can be tuned at the level of DNA, protein, and cooperative protein-protein interactions, necessitating high-throughput experimental approaches for in-depth characterization. Here, we used a cell-free system in combination with a high-throughput microfluidic device to comprehensively study the different tuning mechanisms of a synthetic zinc-finger repressor library, whose affinity and cooperativity can be rationally engineered. The device is integrated into a comprehensive workflow that includes determination of transcription-factor binding-energy landscapes and mechanistic modeling, enabling us to generate a library of well-characterized synthetic transcription factors and corresponding promoters, which we then used to build gene-regulatory networks de novo. The well-characterized synthetic parts and insights gained should be useful for rationally engineering gene-regulatory networks and for studying the biophysics of transcriptional regulation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.