ArticlePloS one2017
Reducing DNA context dependence in bacterial promoters.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 49 citations in OpenAlex.
- Combinatorial Optimization of Protein Systems in Synthetic Cells.ACS synthetic biology · 2026Article
- The adaptive landscapes of three globaleLife · 2026Article
- The highly rugged yet navigable regulatory landscape of the bacterial transcription factor TetR.Nature communications · 2024Article
- Transfer learning for cross-context prediction of protein expression from 5'UTR sequence.Nucleic acids research · 2024Article
- Alteration of the -35 and -10 sequences and deletion the upstream sequence of the -35 region of the promoter A1 of the phage T7 in dsDNA confirm the contribution of non-specific interactions withFrontiers in molecular biosciences · 2023Article
- Functional Synthetic Biology.Synthetic biology (Oxford, England) · 2023Review
- Building the Plant SynBio Toolbox through Combinatorial Analysis of DNA Regulatory Elements.ACS synthetic biology · 2022Article
- LOICA: Integrating Models with Data for Genetic Network Design Automation.ACS synthetic biology · 2022Article
- Synthetic biology and bioelectrochemical tools for electrogenetic system engineering.Science advances · 2022Article
- Massively parallel characterization of engineered transcript isoforms using direct RNA sequencing.Nature communications · 2022Article
- Accurate characterization of dynamic microbial gene expression and growth rate profiles.Synthetic biology (Oxford, England) · 2022Article
- Importance of the 5' regulatory region to bacterial synthetic biology applications.Microbial biotechnology · 2021Review
- Genetic circuit design automation for yeast.Nature microbiology · 2020Article
- The long journey towards standards for engineering biosystems: Are the Molecular Biology and the Biotech communities ready to standardise?EMBO reports · 2020Article
- Programming Escherichia coli to function as a digital display.Molecular systems biology · 2020Article
- Context-dependency of synthetic minimal promoters in driving gene expression: a case study.Microbial biotechnology · 2019Article
- Systematic Evaluation of Genetic and Environmental Factors Affecting Performance of Translational Riboswitches.ACS synthetic biology · 2019Article
- Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically Encoded Multiplexed Reporter Assay in Escherichia coli.Biochemistry · 2019Article
- Utilising datasheets for the informed automated design and build of a synthetic metabolic pathway.Journal of biological engineering · 2019Article
- Designing with living systems in the synthetic yeast project.Nature communications · 2018Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Variation in the DNA sequence upstream of bacterial promoters is known to affect the expression levels of the products they regulate, sometimes dramatically. While neutral synthetic insulator sequences have been found to buffer promoters from upstream DNA context, there are no established methods for designing effective insulator sequences with predictable effects on expression levels. We address this problem with Degenerate Insulation Screening (DIS), a novel method based on a randomized 36-nucleotide insulator library and a simple, high-throughput, flow-cytometry-based screen that randomly samples from a library of 436 potential insulated promoters. The results of this screen can then be compared against a reference uninsulated device to select a set of insulated promoters providing a precise level of expression. We verify this method by insulating the constitutive, inducible, and repressible promotors of a four transcriptional-unit inverter (NOT-gate) circuit, finding both that order dependence is largely eliminated by insulation and that circuit performance is also significantly improved, with a 5.8-fold mean improvement in on/off ratio.
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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.