ReviewNature protocols2017
Compartmentalized partnered replication for the directed evolution of genetic parts and circuits.
Review in Nature protocols, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 26 citations in OpenAlex.
- Leveraging Autonomous Biological Oscillators for Directed Evolution of Switchable Proteins.Advances in experimental medicine and biology · 2026Review
- Directed evolution of L-DOPA sensing and production enables efficient incorporation of an expanded genetic code into proteins.bioRxiv : the preprint server for biology · 2025Article
- Strategies to Expand the Genetic Code of Mammalian Cells.Chemical reviews · 2025Review
- Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology.Biodesign research · 2024Article
- Tuning tRNAs for improved translation.Frontiers in genetics · 2024Review
- Navigating directed evolution efficiently: optimizing selection conditions and selection output analysis.Frontiers in molecular biosciences · 2024Article
- Towards an engineering theory of evolution.Nature communications · 2021Review
- Enhancing n-Butanol Tolerance of Escherichia coli by Overexpressing of Stress-Responsive Molecular Chaperones.Applied biochemistry and biotechnology · 2021Article
- Article
- Roadmap to Building a Cell: An Evolutionary Approach.Frontiers in bioengineering and biotechnology · 2020Article
- Optimized methodology for product recovery following emulsion PCR: applications for amplification of aptamer libraries and other complex templates.Journal of biological methods · 2020Article
- Synthetic evolution.Nature biotechnology · 2019Review
- Trp-ing upon new repressors.Nature chemical biology · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Compartmentalized partnered replication (CPR) is an emulsion-based directed evolution method based on a robust and modular phenotype-genotype linkage. In contrast to other in vivo directed evolution approaches, CPR largely mitigates host fitness effects due to a relatively short expression time of the gene of interest. CPR is based on gene circuits in which the selection of a 'partner' function from a library leads to the production of a thermostable polymerase. After library preparation, bacteria produce partner proteins that can potentially lead to enhancement of transcription, translation, gene regulation, and other aspects of cellular metabolism that reinforce thermostable polymerase production. Individual cells are then trapped in water-in-oil emulsion droplets in the presence of primers and dNTPs, followed by the recovery of the partner genes via emulsion PCR. In this step, droplets with cells expressing partner proteins that promote polymerase production will produce higher copy numbers of the improved partner gene. The resulting partner genes can subsequently be recloned for the next round of selection. Here, we present a step-by-step guideline for the procedure by providing examples of (i) selection of T7 RNA polymerases that recognize orthogonal promoters and (ii) selection of tRNA for enhanced amber codon suppression. A single round of CPR should take ∼3-5 d, whereas a whole directed evolution can be performed in 3-10 rounds, depending on selection efficiency.
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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.