An Open-Source 3D-Printed Vacuum Manifold for Automated DNA Isolation Improves Yields in the Opentrons Flex and OT-2

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 protocols. The automated workflow demonstrated greater plasmid yields and eliminated failed recoveries, though with greater variability in yield between samples. 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.