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YOU CAN BUILD THE 30,000-DOLLAR MACHINE THAT SEPARATES WHOLE CHROMOSOMES, FOR 850 DOLLARS

Build the 30,000-dollar machine that separates whole chromosomes for 850 dollars, with a servo motor and a fixed field instead of switched electrodes.

by Diego Lagos-Susaeta, Oriana Salazar and Juan A. Asenjo

FULL CAD BOM FIRMWARE DOCS

ScienceOpen-hardware

Built withArduino3D printing

difficulty
●●●●●
time
several weekends
license
CERN (hardware), GPL (software), CC BY (documentation)
repo
repo FINISHED0 stars

WHAT YOU’LL NEED

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COMPAREE VERDICT

openPFGE is a published research instrument that does one very specific thing: it separates DNA fragments far too large for ordinary gel electrophoresis, the kind of separation the paper says costs around 30,000 dollars commercially from just two suppliers. The elegant part is the simplification — instead of switching the electric field, a servo motor physically rotates the agarose gel by a set angle (0 to 180 degrees) inside a fixed field in a standard electrophoresis chamber. The paper shows two commercial DNA size markers (up to about 2.2 megabases) run on openPFGE next to the suppliers' reference images, and the cost is about 850 dollars according to the published BOM. This is for someone who already runs agarose gels, knows why they need pulsed-field separation, and has access to a wet lab where they can validate the instrument against known standards. The files are a Zenodo archive and a GitLab project, not an active GitHub repo with discussion threads. You will be sourcing parts yourself from the BOM, printing the gel tray and servo mount, building a small PCB and a Peltier cooling loop. The single thing most likely to go wrong is discovering halfway through that your lab does not actually need whole-chromosome separation. If you do need it, the authors describe it as, to their knowledge, the first fully documented, ready-to-build open-source PFGE.

GOOD TO KNOW

  • —Complete CAD, bill of materials, Arduino firmware and Android app published in the HardwareX paper (DOI 10.1016/j.ohx.2020.e00128) and on Zenodo.
  • —Hardware CERN licensed (open hardware), software GPL, documentation CC BY — all permit commercial use.
  • —Files are hosted on Zenodo (DOI 10.5281/zenodo.3900147) and GitLab, not on a typical GitHub repository.
  • —This is a research publication validated with two commercial DNA size markers compared against the suppliers' reference images, not a community project with ongoing support.
  • —No assembly video, no troubleshooting forum, no supplier recommendations beyond part numbers in the BOM.
  • —You are building scientific instrumentation that handles high voltage and requires wet-lab skills to validate — this is not a beginner electronics project.

Parts to buy

10 items

From our check of the build. Exact quantities and part numbers are in the creator’s BOM.

  • DS3218 digital servoFind
  • Arduino NanoFind
  • HC-05 Bluetooth moduleFind
  • 16x2 I2C LCDFind
  • MOSFETsFind
  • MagnetsFind
  • 12 V peristaltic pumpFind
  • Peltier cooler with fans and water blockFind
  • 12 V/30 A power supplyFind
  • Standard electrophoresis chamber and HV power supplyFind

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Can I build this?

PrintGel tray, tray cover, pins, servo motor support, magnetic motor joint and two hose adapters, printed in PLA or ABS (about 100 g of PLA); everything else is a standard commercial electrophoresis chamber.
BuyDS3218 digital servo, Arduino Nano, HC-05 Bluetooth module, 16x2 I2C LCD, MOSFETs, magnets, 12 V peristaltic pump, Peltier cooler with fans and water block, 12 V/30 A power supply, a standard electrophoresis chamber and HV power supply — full BOM in the paper
ToolsSoldering iron, multimeter, basic hand tools, 3D printer, wet-lab equipment for gel casting and staining, Android device for the control app
SkillsIntermediate electronics (soldering a 12 V Arduino board, Peltier cooling loop), basic Arduino flashing, wet-lab skills (agarose gels, PFGE protocols, DNA staining and imaging), and comfort reading a scientific paper as the primary documentation
TimeSeveral weekends: one for sourcing and verifying parts against the BOM, one for mechanical assembly and enclosure fabrication, one for electronics integration and firmware upload, then calibration and validation runs against known DNA size standards
Cost$$$ — the paper states 850 dollars, but 720 dollars of that is a standard electrophoresis chamber and HV power supply many labs already own; the rotation, cooling and electronics are roughly 130 dollars. Prices will have moved since 2020.
SafetyHigh voltage (electrophoresis power supply, typically 50-200V), ethidium bromide or other DNA stains (mutagens), UV transilluminator for gel imaging (eye and skin hazard). This is laboratory equipment; if you do not already handle these hazards routinely, this is not the project to start with.

Build at your own risk. Projects involve tools, electronics and sometimes mains voltage — follow the creator’s safety notes.

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Gallery

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Start here

Navigation into the creator’s own docs — we don’t rewrite the guide, we route you to the source.

  1. 1.Read the HardwareX paper (The paper is the primary documentation — it explains the design rationale, shows validation results, and contains the full bill of materials)
  2. 2.Download the design files from Zenodo(Zenodo DOI 10.5281/zenodo.3900147 hosts CAD, firmware and Android app; newer versions (updated up to 2022) are on GitLab at gitlab.com/diegusleik/openpfge)
  3. 3.Source parts from the BOM(The BOM is short and mostly generic; parts like the servo are given as examples (a fast, accurate 180-degree digital servo such as the DS3218), and the tray can be adapted to your chamber size — but any change means re-checking your runs against DNA size markers.)
  4. 4.Print the gel tray and servo mount(The FreeCAD files print without supports in PLA or ABS; the servo support attaches to the cover of your electrophoresis chamber, and the design can be adapted to other chamber and gel sizes.)

KNOWN ISSUES

  • This is research instrumentation published in 2020 — part numbers in the BOM may be obsolete, suppliers may have changed, and you will be chasing down equivalents with no community to ask.
  • The paper assumes you already know why you need pulsed-field gel electrophoresis and how to validate it; if you have never run ordinary agarose gels or separated genomic DNA, start there first.
  • The run uses a commercial electrophoresis high-voltage supply on a buffer-filled chamber, and the cooling loop pumps that buffer next to mains-powered electronics. Follow the paper's safety notes: isolate the 12 V supply's mains side, keep buffer away from the circuit, and only switch on the HV supply with the chamber closed.
  • Gel rotation must be smooth and repeatable, and the tray must sit level about 1 cm above the chamber floor. Check your build the way the authors did: run a commercial DNA size marker under the supplier's recommended conditions and compare it with the supplier's reference image.
  • The Android app was published on Google Play, but the listing is no longer live; the source (targeting Android 8–10) and a release bundle are on GitLab, so expect to build or sideload it yourself.
  • No troubleshooting guide or user forum, and the GitLab repo has been quiet since 2022 — treat it as a published design, not an ongoing project with a community.

What is pulsed-field gel electrophoresis and do I actually need it?

PFGE separates DNA fragments larger than about 30-50 kilobases, up to whole chromosomes several megabases long. Ordinary gel electrophoresis fails at that scale because all large fragments move at the same speed. You need it if you are separating bacterial chromosomes, doing genomic mapping, or typing strains by whole-genome restriction digest. If your DNA is shorter than 30kb, ordinary agarose gel electrophoresis is simpler and this project is overkill.

Can I build this without access to a wet lab?

No. You need to cast agarose gels, prepare running buffer, load DNA samples, stain the gel after the run, and image it under UV — all standard molecular biology techniques. More importantly, you need known DNA size standards to validate that the instrument is actually working, which means access to a freezer, pipettes and reagents. This is not a garage electronics project.

How does rotating the gel compare to the commercial switched-electrode design?

Both reorient the electric field across the gel so large DNA molecules have to keep turning. Bio-Rad's CHEF switches the field electronically, and Analytik Jena's Rotaphor physically rotates the electrodes. openPFGE keeps the field fixed and rotates the gel itself with a servo, which needs far simpler electronics. The authors report similar applications, maximum resolved fragment size and run times to commercial equipment, while calling it a first version.

The paper says 850 dollars — is that still realistic?

Published in 2020; electronics prices have moved, some parts may be discontinued, and you will almost certainly pay more for small-quantity hobbyist sourcing than a university lab with supplier accounts. Treat it as an order-of-magnitude estimate, not a hard budget. The electrophoresis chamber and high-voltage power supply are about 720 dollars of the total — if your lab already has them, the build itself is closer to 130 dollars.

Is there any commercial support or calibration service?

No — this is an open source research publication, not a product. Calibration is your responsibility, using your own DNA size ladders and your own validation protocol. The paper shows their validation results, but you are on your own.

Community builds

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Discussion1

FROM THE COMPAREE TEAM

Commercial PFGE from Bio-Rad or Analytik Jena costs around 30,000 dollars according to the paper, and the authors name only those two suppliers — openPFGE costs about 850 dollars and rotates the gel with a servo instead of switching electrodes. If you have run agarose gels before: what would you actually use whole-chromosome separation for?

CompareeTEAM17d agoedited

Practical notes from our verification: this is a 2020 research publication in HardwareX, not a live GitHub project with issues and pull requests — the files are on Zenodo (DOI 10.5281/zenodo.3900147) and GitLab, where the last commit dates from 2022. The paper itself is the documentation, and it is detailed: a BOM with part numbers, 3D printable gel-rotation parts, the PCB design, Arduino firmware and the Android app, plus validation runs of two commercial DNA size markers compared against the suppliers' reference images. Note that most of the cost is off-the-shelf lab equipment: a standard electrophoresis chamber and a commercial high-voltage power supply account for roughly 720 of the 850 dollars. The single biggest thing to know before starting is that this is laboratory instrumentation that requires wet-lab skills to validate — if you do not already run gels and work with genomic DNA, the electronics are the easy part and the molecular biology is where it will go wrong. No commercial suppliers offer assembled units, and the BOM prices are from 2020 — expect to spend time finding current equivalents for some parts. Correction (4 October 2026): we re-checked this page line by line against the project's own repository, documentation and videos, and fixed errors in earlier versions.

Diego Lagos-Susaeta, Oriana Salazar and Juan A. Asenjo

Researchers at the Centre for Biotechnology and Bioengineering, Department of Chemical Engineering, University of Chile. They published openPFGE in HardwareX in 2020 as a response to the 30,000-dollar cost and two-supplier monopoly on commercial PFGE equipment, with the explicit goal of making whole-chromosome separation accessible to labs that cannot afford commercial systems.

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