I’ve been designing a PCR thermocycler since late fall 2017. My personal microbiology and rose hybridization hobbies have taken a route into genetics. Frustrated at not finding a suitable machine under $2000 I made the decision that this could be something that I should be able to build myself for less than $200.
How hard could it be to heat and cool 24 microtubes of water anyways, right?
It turned out to be quite a bit harder than I thought it would be and I probably blew through my 200$ budget some time ago.
What is a thermocycler?
A thermocycler heats and cools liquids inside of microtubes quickly according to a pre-programmed sequence of steps to rapidly replicate DNA. A common protocol might be to have an initial denaturalization stage of 95c to break the hydrogen bonds and separate DNA into two strands for 5 seconds, followed by an annealing stage at 45c to allow DNA primers to attach to the strands for 10 seconds, followed by an extension stage at 72c to produce the new DNA. Performed over and over many copies of a DNA sample can be created.
Originally water baths were used for this purpose; but this requires a great deal of manual labor and may potentially introduce contamination into the sample.
The challenge with a thermocycler is the speed at which those temperature changes need to occur. Commercial thermocyclers advertise rates of 6c/sec. The thermocycler I built has a rate of 1c/sec to 1.5c/sec.
Current Design
For my DYI Thermo cycler I used the following primary components:
- Heating Block; Aluminum 250g: Heating Block for Minit-100 Dry Bath, Lab Heat Block for 0.5 Ml Tubes
- TEC: TEC1–12710 Thermoelectric Peltier Cooler 12V 100W 154Wmax
- Heat Sink: 2 x Cooler Master Hyper 212 EVO RR-212E-20PK-R2 CPU Cooler with 120mm PWM Fan
- Arduino Relay Shield: RobotDyn — Relay Shield with opto-isolation and prototyping area for Arduino Uno, Mega, Leonardo. 4 channels
- Arduino Uno
- MD30C Cytron 30A DC Motor Driver
- 3x DS18B20 100cm with Heat Resistance Thermal Cable and Stainless Steel Probe
Heating Block
Originally I purchased an aluminum heat block which originally had a mass of roughly 650g. I peppered the heat block with holes and brought the overall mass down to 500g, but I still could not achieve a temperature rate change greater than .25c/secs.
The heat block currently in use weighs is another dry-bath heating block which weighs 250g on the dot. There’s no real room to cut mass on this block.
There is significant room for improvement in the heating block, and many discussions were had to determine how this component could be optimized. The overall goal is to reduce thermal mass and increase thermal conductivity. In the end I decided to build the cycler in a way which would allow me to replace the block later should I need to do so.
Some of the ideas for improvements have included:
- Switching to silver and having it 3D printed ( Expensive )
- Using copper bar and welding copper tube sections vertically to hold the samples ( Time consuming )
- Improve the mounting of the heat block to the TEC/Heat sink.
- Finally heat the copper lid and have it independently monitored for temp
Heat Sink And Control System
While the heat sink itself is relatively standard it is important to understand that in order to optimize the system you actually need to preserve a significant amount of heat intentionally to minimize the difference between the cool and hot side of the TEC. The two 120mm heat sinks are enormous and they sit side-by-side. One of the fans on a heat sink has been reversed to allow, when desired, rapid exhaust of the heat within the heat sink. The entire set of heat sinks is then insulated and one of the temperature probes has been inserted to allow for monitoring the heat-sink temperature.
The curious thing is that while the ultimate goal is to control the temperature of the heating block according to a predefined program, managing the temperature of the heat sink is the real challenge. TECs work on a differential between the two sides of the device. The closer in temperature of the heat sink to the heating block the less work the TEC needs to perform. The two sides of the TEC need to be well-isolated from one-another and if thermal paste is used compression should be applied to improve the contact.
My simple rules for the control system include:
- Use proportional control when approaching the target temperature (the change is too rapid for full PID control)
- Only use the fan when cooling the system
- Pre-cooling the heat sink before a cool-down phase improves cooling time.
- Pre-heating the heat sink before a ramp-up in temperature improves ramp up time. ( Not implemented )
Future Improvements:
- Add an additional, 100w heater for pre-heating the heat sink. This is essentially a little hair-dryer heater, and it would be positioned to flow in through the side of the insulation on the heat sink.
- Improvements to the proportional control get better temperature stability
Code is available.
Performance:
The current design can still undershoot the low temperature range on a protocol such as:
- 95c for 5 seconds
- 45c for 10 seconds
- 72c for 15 seconds
This is essentially a worst-case scenario with long ramp times. The proportional control can be significantly improved to introduce more stability, but that would come at the cost of increased ramp time as the target temperature is approached.
Conclusion
There’s a number of improvements that can be made to this existing device. The current design allows me to modify the control program at will ( all output is serial ), replace the heat block, and add additional heaters where needed. This is a good starting place.
