This tutorial will show you how to make a thermal cycler from scratch for about $85. In short, PCR (polymerase chain reaction) amplifies bits of DNA, creating millions of copies of a target sequence. You can use it to test a DNA sample for a specific gene, for instance, to check for genetic modification in food and for hereditary gene testing.
During PCR, a mixture of DNA, primer and DNA polymerase is cycled between three different temperature settings, over and over again. This project uses an arduino to control two high-power resistors to heat up the sample, a computer fan to cool down, and a thermocouple to keep track of the temperature. The design supports two samples at a time, though it could probably be extended to support more.
The parts are all off-the shelf, and the assembly should take a few hours. You will need access to a shop (at the very least a ban saw and drill press).
This project is still a work in progress by Stacey Kuznetsov (stace@cmu.edu) and Matt Mancuso (mcmancuso@gmail.com). Please email us if you have any questions or feedback! Also, huge thanks to Rich Pell, James Lata and the ATX Hackerspace for materials & feedback.
During PCR, a mixture of DNA, primer and DNA polymerase is cycled between three different temperature settings, over and over again. This project uses an arduino to control two high-power resistors to heat up the sample, a computer fan to cool down, and a thermocouple to keep track of the temperature. The design supports two samples at a time, though it could probably be extended to support more.
The parts are all off-the shelf, and the assembly should take a few hours. You will need access to a shop (at the very least a ban saw and drill press).
This project is still a work in progress by Stacey Kuznetsov (stace@cmu.edu) and Matt Mancuso (mcmancuso@gmail.com). Please email us if you have any questions or feedback! Also, huge thanks to Rich Pell, James Lata and the ATX Hackerspace for materials & feedback.
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Signing UpStep 1: More on PCR
To run PCR, you need DNA, primers that match the sequence you're trying to replicate and polymerase.
PCR consists of 3 steps that are cycled over and over again:
Denaturation (~94C) At this step, DNA 'breaks apart', splitting from a double helix into single strands
Annealing (~60C) Primers bond to the single-stranded DNA
Extension (~72C) Polymerase compliments the DNA, synthesizing strands that are of the target sequence
Each of these phases can be 20-30 seconds long and repeated 30+ times, depending on the protocol. Most protocols also suggest having a longer initial denaturation step and a longer final extension step.
A simple tutorial:
http://www.dnalc.org/resources/animations/pcr.html
There's also a bunch of related resources here: http://www.lab-manual.com/lm_209.htm
The results of PCR can be visualized using gel electrophoresis. DNA samples are loaded into a gel, and a high voltage is applied across it. Because DNA is negatively charged, it will travel through the gel at different speeds depending on its size. This process will effectively separate out the pieces you want, and you can see them by staining the gel. Here's a good tutorial and if you're trying to DIY it, the Macgyver Project is a pretty good resource.
PCR can be performed using 3 water baths (each kept at one of the three temperature settings). A human could physically move the samples from one bath to the next 30+ times. PCR machines were developed to automate the process, but most lab-quality ones cost thousands of dollars. But they don't need to! Today there is a growing number of open source PCR projects, among them OpenPCR (600$), LavaAmp ($200), and the Coffee Cup PCR (350$).
PCR consists of 3 steps that are cycled over and over again:
Denaturation (~94C) At this step, DNA 'breaks apart', splitting from a double helix into single strands
Annealing (~60C) Primers bond to the single-stranded DNA
Extension (~72C) Polymerase compliments the DNA, synthesizing strands that are of the target sequence
Each of these phases can be 20-30 seconds long and repeated 30+ times, depending on the protocol. Most protocols also suggest having a longer initial denaturation step and a longer final extension step.
A simple tutorial:
http://www.dnalc.org/resources/animations/pcr.html
There's also a bunch of related resources here: http://www.lab-manual.com/lm_209.htm
The results of PCR can be visualized using gel electrophoresis. DNA samples are loaded into a gel, and a high voltage is applied across it. Because DNA is negatively charged, it will travel through the gel at different speeds depending on its size. This process will effectively separate out the pieces you want, and you can see them by staining the gel. Here's a good tutorial and if you're trying to DIY it, the Macgyver Project is a pretty good resource.
PCR can be performed using 3 water baths (each kept at one of the three temperature settings). A human could physically move the samples from one bath to the next 30+ times. PCR machines were developed to automate the process, but most lab-quality ones cost thousands of dollars. But they don't need to! Today there is a growing number of open source PCR projects, among them OpenPCR (600$), LavaAmp ($200), and the Coffee Cup PCR (350$).
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Also, have you heard of the dremelfuge? It's an attachment for a standard rotatory tool or power drill which can generate pretty significant centrifugal acceleration. Figured you might appreciate hearing about it, if you hadn't already.
Keep up the good work.
If the RMs is 120, the peak voltage is 120*sqrt(2)=169.706
so for a large fraction of the operating time, the resistors will be getting above 120 volts, all the way up to 170 volts.
I=V/R I=170/300 I=.56
P=VI P=170*.56 P=68 watts
Although you are not operating at 170 volts all of the time, you are exceeding the wattage rating for a significant amount of time every second. I sincerely suggest you use 100 watt resistors. These will protect you from peak voltage as well as any power surge/ripple.
Besides that, I love the product! I am currently working in a bio lab with fancy thermo cyclers and they are essential to our work.
I am sure you can large wattage wirewound resistors on the internet. Good luck.
The RMS value is THE SAME HEATING value as the equivalent DC. FORGET the peak.
Your numbers are completely wrong. We cannot talk about "peak power", there is no such thing.
Steve
I = 170/600 = 0.28A
P=170*.28 = 48Watts (at peaks)
Does that seem right?
However, to guarantee proper operation and long life, you might want to go even higher. Resistor wattage ratings are usually absolute maximum ratings which can be tolerated for only a short amount of time. With 300 ohm resistors, you go to 96% of the absolute maximum it would likely receive. In the name of caution, I only use resistors at up to 1/2 to 2/3 their rated wattage capacity. Depending on price and availability, I would recommend a total resistance of more than 750 ohms, this will place you below 40 watts at peak.
A few reasons for this caution are outlined below.
The tolerance on your wattage may be several percent, so your capacity could be from 47.5 to 52.5 watts with a 5% tolerance. Unfortunately tolerance on wattage is less prevalent than tolerance on resistance.
Also, grid surges and ripples do occur and you want to build your device to handle the worst case scenario.
It is good practice to err on the side of caution and never trust your components.
For power of 40W - implies 120mA current
Resistors would be 2.6 kOhm.
Using preferred values:
- two 1500 Ohms resistors (choose devices with 25W or greater rating. Preferably 40W)
- gives us 110mA and 35 Watts.
or: - two 1200 Ohm resistors (choose devices with 30W minimum ratings. Preferably 40-50W)
- gives us 135mA at 44 Watts.
Use an osPID to control the SSR driving the load.
Use a cheap (low temp 400C) k-type thermocouple to connect to the osPID controller.
Cool project, I'll make one.
mac
The project uses the arduino PID library. You might want to check it out.
Works perfectly for me. Ramp controls and everything.
How tightly does the conical section of the PCR tube fit into the heating block? Do you add a liquid or gel to transfer heat between the heater block and the PCR tube when the tube is in the block?
Do you add mineral oil on top of the PCR reaction mix to prevent condensation in the cap of the PCR tube?
I've seen a couple of other DIY PCR projects. We should get some funds (Kickstarter? a grant?) to manufacture drill bits for milling out the precise profile of a PCR tube. I'd use one. I bet you'd use one... wonder how much a batch of 20 would be.
The PCR tube sits really tightly circumference-wise, but the conical section is not tight at all :( We just used a regular drill bit, so our holes are a little longer than the height of the tube. Adding a gel/liquid to speed up heat transfer is a great idea, is there a material you recommend?
Yes, def using mineral oil since there's no heated lid.
A custom-drill bit might be nice. I found this: http://www.wolftooltech.com/Single_Diameter_Carbide_Drill_Quote_Request_Form.pdf I could send in a quote, but if you're trying to build something for under $100, or preferably even under $50, it has to cost like $5-10 or it's probably not worth it...
It would be neat to find a $10 milling tool set that could be used to drill out the block. Maybe a standard tapered ball-point end mill & a cylindrical drill bit? Not sure.
Alternatively someone could have a bunch of 8-tube strip, 16-well, and 48-well blocks manufactured and sold near cost.
Without a base resistor, your base voltage wants to sit at ~1 volt and your Arduino pin wants to be at 5v. This makes your Arduino unhappy.
Great project nonetheless!
Why not use an "off the shelf" heat sink?
Wouldn't the SCR last longer if it was mounted on a heat sink?
Why not use "off the shelf" heater cartridges instead of those resistors?
When you figure out how to add optics, you'll really have a platform to outcompete the big boys!