ArticleSynthetic biology (Oxford, England)2023
AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots.
Article in Synthetic biology (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 40 citations in OpenAlex.
- Vision and Development of a Design, Implementation, and Verification Automation (DIVA) Software Platform for DNA Construction.ACS synthetic biology · 2026Article
- Automated linear DNA assembly of A. thaliana's chloroplast and mitochondrial genome.Nucleic acids research · 2026Article
- Slowpoke: An Automated Golden Gate Cloning Workflow for Opentrons OT-2 and Flex.ACS synthetic biology · 2026Article
- Modification of a Low-Cost Pipetting Robot for Nanoliter Liquid Handling and Autosampling for Liquid Chromatography-Mass Spectrometry.Journal of separation science · 2026Article
- High-throughput yeast engineering in biofoundries: towards autonomous and scalable synthetic biology.FEMS yeast research · 2026Review
- CloneCoordinate: Open-Source Software for Collaborative DNA Construction.ACS synthetic biology · 2025Article
- Directed assembly of single-stranded DNA fragments for data storage via protein-free catalytic splint ligation.Nucleic acids research · 2025Article
- ActinoMation: A literate programming approach for medium-throughput robotic conjugation ofSynthetic and systems biotechnology · 2025Article
- The knowledge driven DBTL cycle provides mechanistic insights while optimising dopamine production in Escherichia coli.Microbial cell factories · 2025Article
- Semi-automated workflow for high-throughput Agrobacterium-mediated plant transformation.The Plant journal : for cell and molecular biology · 2025Article
- Biofoundry-Assisted Golden Gate Cloning with AssemblyTron.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Engineering biology and automation-Replicability as a design principle.Engineering biology · 2024Review
- Genetically Encoded, Noise-Tolerant, Auxin Biosensors in Yeast.ACS synthetic biology · 2024Article
- Getting the Right Clones in an Automated Manner: An Alternative to Sophisticated Colony-Picking Robotics.Bioengineering (Basel, Switzerland) · 2024Article
- Automated in vivo enzyme engineering accelerates biocatalyst optimization.Nature communications · 2024Review
- TidyTron: Reducing lab waste using validated wash-and-reuse protocols for common plasticware in Opentrons OT-2 lab robots.SLAS technology · 2024Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As one of the newest fields of engineering, synthetic biology relies upon a trial-and-error Design-Build-Test-Learn (DBTL) approach to simultaneously learn how a function is encoded in biology and attempt to engineer it. Many software and hardware platforms have been developed to automate, optimize and algorithmically perform each step of the DBTL cycle. However, there are many fewer options for automating the build step. Build typically involves deoxyribonucleic acid (DNA) assembly, which remains manual, low throughput and unreliable in most cases and limits our ability to advance the science and engineering of biology. Here, we present AssemblyTron, an open-source Python package to integrate j5 DNA assembly design software outputs with build implementation in Opentrons liquid handling robotics with minimal human intervention. We demonstrate the versatility of AssemblyTron through several scarless, multipart DNA assemblies, beginning from fragment amplification. We show that AssemblyTron can perform polymerase chain reactions across a range of fragment lengths and annealing temperatures by using an optimal annealing temperature gradient calculation algorithm. We then demonstrate that AssemblyTron can perform Golden Gate and homology-dependent
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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.