ArticleNucleic acids research2017
Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 20 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
20 citing papers in PubMed.
- Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.Nucleic acids research · 2024Article
- Engineering is evolution: a perspective on design processes to engineer biology.Nature communications · 2024Article
- Machine Learning-Guided Optimization ofACS synthetic biology · 2024Article
- Toolbox of Characterized Genetic Parts forACS synthetic biology · 2024Article
- Systematic Part Transfer by Extending a Modular Toolkit to Diverse Bacteria.ACS synthetic biology · 2023Article
- Genetic circuit design automation with Cello 2.0.Nature protocols · 2022Review
- PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies.ACS synthetic biology · 2022Article
- 15 years of microbial biotechnology: the time has come to think big-and act soon.Microbial biotechnology · 2022Article
- Surveying the Genetic Design Space for Transcription Factor-Based Metabolite Biosensors: Synthetic Gamma-Aminobutyric Acid and Propionate Biosensors inFrontiers in bioengineering and biotechnology · 2022Article
- Synthetic living machines: A new window on life.iScience · 2021Review
- Harnessing the central dogma for stringent multi-level control of gene expression.Nature communications · 2021Article
- Removing the Bottleneck: Introducing cMatch - A Lightweight Tool for Construct-Matching in Synthetic Biology.Frontiers in bioengineering and biotechnology · 2021Article
- Article
- A 'poly-transfection' method for rapid, one-pot characterization and optimization of genetic systems.Nucleic acids research · 2019Article
- Targeting individual cells by barcode in pooled sequence libraries.Nucleic acids research · 2019Article
- The art of vector engineering: towards the construction of next-generation genetic tools.Microbial biotechnology · 2019Review
- MetClo: methylase-assisted hierarchical DNA assembly using a single type IIS restriction enzyme.Nucleic acids research · 2018Article
- Scaling up genetic circuit design for cellular computing: advances and prospects.Natural computing · 2018Article
- Automated Robotic Liquid Handling Assembly of Modular DNA Devices.Journal of visualized experiments : JoVE · 2017Article
- Engineering biological systems using automated biofoundries.Metabolic engineering · 2017Review
Corrections and comments
- Erratum issued
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genetic designs can consist of dozens of genes and hundreds of genetic parts. After evaluating a design, it is desirable to implement changes without the cost and burden of starting the construction process from scratch. Here, we report a two-step process where a large design space is divided into deep pools of composite parts, from which individuals are retrieved and assembled to build a final construct. The pools are built via multiplexed assembly and sequenced using next-generation sequencing. Each pool consists of ∼20 Mb of up to 5000 unique and sequence-verified composite parts that are barcoded for retrieval by PCR. This approach is applied to a 16-gene nitrogen fixation pathway, which is broken into pools containing a total of 55 848 composite parts (71.0 Mb). The pools encompass an enormous design space (1043 possible 23 kb constructs), from which an algorithm-guided 192-member 4.5 Mb library is built. Next, all 1030 possible genetic circuits based on 10 repressors (NOR/NOT gates) are encoded in pools where each repressor is fused to all permutations of input promoters. These demonstrate that multiplexing can be applied to encompass entire design spaces from which individuals can be accessed and evaluated.
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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.