Portable DNA Thermocycler

This is a small thermocycler used for running PCR reactions. It includes a tool for visualizing fluorescence too. It can be used for running CDC approved Taqman tests for SARS-CoV-2.

The system includes: 

  1. Milled thermoblock and case for holding PCR tubes
  2. Illuminated tube holder for fluorescence imaging using something like a cell phone camera
  3. Arduino microcontroller shield for controlling heater, Peltier cooling system, and reading a temperature sensor
  4. Simple open-source command-line python based software for thermocycling and turning on blue LED (Works on Windows, Mac and Linux)
  5. 12 PCR tubes that can be washed and reused
  6. Mineral oil
  7. Power supply
  8. 1 pipettor module, 6 wide bore pipettes, and 6 10ul reaction volume pipettes details
Thermocycler for portable PCR detection
CAD view of the thermocycler assembly. It has an imaging station for visualizing fluorescence using something like a cell phone camera. When the Taqman probe binds to the amplified sequence the color change goes from red to green.
PCR thermocycler for decentralized nucleic acid testing
Picture of what the thermocycler device looks like. Its made using 3D printer parts (ie., heaters, thermistor, electronics and Arduino based firmware)

Portable thermocycler and imaging station for cell phones

The LED excites the fluorochrome and gets you to see if the target sequence is amplified

The Green channel was plotted to compare. Heat conditions:

  • 95C 15 seconds
  • 60C 30 seconds
  • 40 cycles


    1. beta-actin – PCR with Taqman probe
    2. blank – water control with master mix

Note: after 30 cycles signal was visible

Nucleic acid detection using Taqman probe PCR using a thermocycler made from 3D printed parts
Example of Taqman PCR using a thermocycler made using parts of a 3D printer extruder
Taqman probe visualization using cell phone camera
Example of what the amplfied signal looks like when running a Taqman probe based PCR. When the probe binds to the amplified target sequence the signal shifts from red to green

Pipetting setup for decentralized Taqman probe PCR 

Low cost pipetting tools for cecentralized PCR detection
The system shown consists of a reaction master mix tube that can contain the sample, mineral oil tube (for keeping the reaction mix at bottom of PCR tube during thermocycling), pipettor tool, wide-bore pipette for aspirating and dispensing mineral oil, and a small volume pipette for aspirating and dispensing the reaction master mix. Also shown are PCR tubes that fit in the PCRmon thermocycler. The mineral oil is layered on top of the aspirated reaction mix.
low cost pipetter design for remote nucleic acid testing
The pipettor is able to securely attach to different types of pipette tips. By squeezing the top part of the silicone tubing, it is possible to aspirate and dispense very small volumes. To consistently aspirate the same volume, a marking on the pipette tip can be drawn as a reference.
Marked pipette tips make it easy to accurately aspirate volumes
In order to transfer the reaction from the source well into the PCR test tube, you need to aspirate then dispense the sample. This example demonstrates how it is easy to accurately aspirate microliter volumes of reaction mix (in this action the volume aspirated is 10µl). In order to aspirate, first, you squeeze the tubing at the top of the pipette using your index finger and thumb in order to reduce the volume in the pipette, then you move the pipette into the tube containing the reaction mix that you want to aspirate and carefully reduce the squeezing pressure in order to create suction to aspirate the volume enough to reach the marketing. Then you move the pipette tip to the empty PCR tube and dispense the volume.
Mineral oil aspirator for remote nucleic testing using a thermocycler
Because the PCRmon thermal block does not have a heated lid, mineral oil is needed in order to keep the volume of the reaction mix at the bottom of the PCR tube during thermocycling. The smaller pipettes used for aspirating the reaction mix have too small of an orifice for this relatively viscous mineral oil so a larger bore pipette tip is better for this. The volume of the mineral oil added to the reaction mix is not as critical, you can aspirate the total amount of volume (just squeeze and release entirely when the pipette tip is in the mineral oil), this produces around 30μl of mineral oil in the tube.