---
title: "Open-source 3D-printed vacuum manifold for automated spin-column DNA isolation on Opentrons"
id: "biorxiv-1-an-open-source-3d-printed-vacuum-manifold-for-automated-dna-isolation-in-the"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-1-an-open-source-3d-printed-vacuum-manifold-for-automated-dna-isolation-in-the"
content_type: "clinical_feed_article"
specialty: "General"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.09.16.746974v1?rss=1"
published_at: "2026-09-21T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Open-source 3D-printed vacuum manifold for automated spin-column DNA isolation on Opentrons
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-1-an-open-source-3d-printed-vacuum-manifold-for-automated-dna-isolation-in-the
- **Specialty:** [General](https://medichelpline.com/clinical-feed/general.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.09.16.746974v1?rss=1)
- **Published At:** 2026-09-21T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The authors developed an open-source, 3D-printed **vacuum manifold** that works with Opentrons Flex and OT-2 liquid-handling robots to automate **spin-column DNA isolation**. - The device supports automated processing of up to **24 samples per run** and can be scaled to **96 samples** by linking four manifolds in series. - The manifold is printable in standard ABS filament and can be manufactured for approximately **$2**, using widely available spin-columns and no specialist reagents. - Compared with manual centrifugation and vacuum protocols, the automated workflow reduced hands-on time for 24 plasmid minipreps by **80%**. - The automated protocol produced comparable or greater plasmid yields and eliminated failed recoveries reported with manual methods. - All design files, labware definitions, and Opentrons protocols are publicly released under the **CERN Open Hardware Licence** or **MIT License**, increasing reproducibility and accessibility. - The work targets academic laboratories that need occasional high-quality DNA extractions without investing in costly magnetic separation modules or specialist kits. - The authors are Jack AT Dalton, Caleb Goddard, and Jean-Baptiste AT Lugagne (University of Oxford). The preprint was posted September 21, 2026, with DOI https://doi.org/10.64898/2026.09.16.746974 and associated Zenodo record https://doi.org/10.5281/zenodo.21674775. - Funding was declared from the Engineering and Physical Sciences Research Council (EP/Y034791/1). The authors declared no competing interests.
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Jack AT Dalton University of Oxford * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Jack%2BAT%2BDalton%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Dalton%20JA&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AJack%2BAT%2BDalton%2B) * [ORCID record for Jack AT Dalton](http://orcid.org/0009-0000-3095-5404 "Open in new tab") * For correspondence: jackdalton83@gmail.com Caleb Goddard University of Oxford * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Caleb%2BGoddard%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Goddard%20C&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ACaleb%2BGoddard%2B) Jean-Baptiste AT Lugagne University of Oxford * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Jean-Baptiste%2BAT%2BLugagne%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Lugagne%20JA&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AJean-Baptiste%2BAT%2BLugagne%2B) * [ORCID record for Jean-Baptiste AT Lugagne](http://orcid.org/0000-0002-8374-6590 "Open in new tab") * [Abstract](https://www.biorxiv.org/content/10.64898/2026.09.16.746974v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5799047/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.09.16.746974v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5799047/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.09.16.746974v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5799047/1) * [Data/Code](https://www.biorxiv.org/content/10.64898/2026.09.16.746974v1.external-links)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_data_code/node:5799047/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.09.16.746974v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5799047/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract Laboratory automation is increasingly being adopted in academic research to improve throughput, reproducibility, and integration with computational workflows. A common bottleneck in molecular biology workflows is the isolation of DNA, typically performed with spin-column kits relying on centrifugation or vacuum. Existing automation solutions depend on magnetic separation systems requiring costly additional modules and specialist kits, making them impractical for laboratories that perform large numbers of extractions only occasionally. Here we present an open-source, 3D-printed vacuum manifold compatible with the Opentrons family of liquid handling robots that enables automated spin-column DNA isolation for up to 24 samples per run (96 with four manifolds in series). The manifold can be manufactured for approximately $2 using standard ABS filament and is compatible with widely available spin-columns, requiring no additional specialist reagents. Using this system, hands-on time for 24 plasmid minipreps was reduced by 80% compared to manual centrifugation and vacuum protocols. The automated workflow demonstrated comparable or greater plasmid yields and eliminated failed recoveries. All design files, labware definitions, and Opentrons protocols are released under the CERN Open Hardware Licence or MIT License. This device lowers the cost barrier to automated DNA purification for academic laboratories worldwide. ### Competing Interest Statement The authors have declared no competing interest. ## Footnotes * ## Funder Information Declared Engineering and Physical Sciences Research Council, https://ror.org/0439y7842, EP/Y034791/1 Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a [CC-BY 4.0 International license](http://creativecommons.org/licenses/by/4.0/). bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. 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[ Download PDF](https://www.biorxiv.org/content/10.64898/2026.09.16.746974v1.full.pdf) Print/Save Options [Download PDF](https://www.biorxiv.org/content/biorxiv/early/2026/09/21/2026.09.16.746974.full.pdf)Full Text & In-line FiguresXML [More Info](https://www.biorxiv.org/about/FAQ#PrintOptions "More Information on Print/Save Options") [ Data/Code](https://www.biorxiv.org/content/early/2026/09/21/2026.09.16.746974.external-links) [ Email](https://www.biorxiv.org/ "Email this Article") [ Share](https://www.biorxiv.org/) An Open-Source 3D-Printed Vacuum Manifold for Automated DNA Isolation in the Opentrons Flex and OT-2 Jack AT Dalton, Caleb Goddard, Jean-Baptiste AT Lugagne bioRxiv 2026.09.16.746974; doi: https://doi.org/10.64898/2026.09.16.746974 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. 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