PCR Machines and Democratizing Science

Photo by Arnaud Jaegers on Unsplash

If I told you to create a full genetics lab, stacked with all the necessary tools to create the cure for any disease, the cost would be in the thousands if not tens of thousands of dollars. Funding is the biggest issue in the scientific world. Every other issue stems from the need to get money: Conflicts of interest, failed studies, and lack of information all stem from the need to get money. Cheap, good, equipment is the number one concern for these labs, and it seems harder and harder to sate that concern every day. One piece of equipment is a PCR Machine, otherwise known as a thermal cycler.

What is PCR?

PCR stands for Polymerase Chain Reaction. Any “-ase” simply means an enzyme, or a biological catalyst. Polymerase’s function is to synthesize DNA, and is part of a three step process: Denaturing, Annealing, and Elongation:

Photo by Tomas Sobek on Unsplash
  1. Denaturing: DNA is found in a double helix, with hydrogen bonds holding the bases together. Just as a zipper would, an enzyme called DNA Helicase breaks these hydrogen bonds, creating two separated helices of DNA.
  2. Annealing: These strands of DNA have two ends signifying what to amplify; the 3' end. and the 5' end. PCR Primers, or single stranded DNA around 20 nucleotides in length, are then utilized. They start from the 3' end, which means that these primers will go in the opposite direction. They will both start from the 3' end and go towards the 5' end, but they will be the opposite. They essentially imitate the other strand of DNA.
  3. Extension: From here, Taq Polymerase does the job that the primers started and synthesizes the segment of DNA fully. There are now two strands of DNA. This process can be repeated ad nauseum.
Regular DNA
Primers added, going in the direction from 3' to 5'
Synthesis of DNA

The Uses

Now, there has to be a point for replicating DNA. The biggest use for PCR is with DNA sequencing and classification as a whole.

  • Sanger Sequencing utilizes amplifying unknown sequences of DNA to get a larger, more accurate picture of the entire genome.
  • Forensics uses PCR for genetic fingerprinting, comparing different types of DNA fragments together. This could be for crime scenes, but it could also be used to analyze ancient DNA!
  • Virus Detection is also possible; traces of the virus can be amplified to show a clear distinction of the virus in DNA.
  • The easiest way to test for COVID-19 is with a PCR test, using the virus detection method to see genetic sequences unique to COVID-19.
Photo by CDC on Unsplash

PCR Machines

The way that this biological process combines with engineering is with a PCR Machine. Other synonyms for these machines are Thermal Cyclers. Now, thermal means heat, which means that this machine cycles through heat. To echo the PCR process, these machines cycle from (94C–96C)—(94C-98C) —(50C–65C) for the Denaturing, Annealing, and Extension stages respectively. This process takes around 45 minutes for 20 cycles for the high end machines, creating just north of a billion segments. This time usually is determined by the strength of the machine.

Photo by Element5 Digital on Unsplash

Democratization

Although the technology seems simple enough, these machines are expensive. Many of the high end machines cost anywhere from $10,000 to $30,000. Even the cheaper ones come in the thousands, and only the simplest of machines come under $1K. This is a cost that is too high considering the plethora of important uses. In poorer hospitals across the world where essentials come in low supply, there is no justification for new technology. In the past century, medicine has preferred prevention over treatment, and a PCR machine is necessary for modern day prevention. Because of the high upfront cost, the possibilities of cheaper medicine are locked away from the poor. There must be a way to democratize these machines.

The Barebones

At it’s core, a PCR machine is just an adjustable oven that has to be accurate. To control it, a microcontroller takes the hem in order to create a cheaper system. Many of these microcontrollers come under $10 or even $5 depending on the type. These microcontrollers have to be controlled by a computer in order to get both data. From there, specific parts must be attached to create the temperature cycles, including an orientation sensor, temperature regulators, and an actual vessel with insulation. This can bring the cost of the PCR to a ceiling of around $100. Certain parts may not be as efficient, but DNA replication can happen in 2 figures.

My attempt

Although I tried to replicate DNA with my own PCR machine, I was quickly left lost. I had little experience with circuitry, and my coding experience couldn’t translate easily. Although I couldn’t get a working machine going, I was able to get the circuitry ready.

The core components:

  • A microcontroller (I’d use an Arduino Uno)
  • A breadboard (where the circuit is placed)
  • A power source
  • Data collection
  • Temperature adjusters, including a fan and heaters
  • Indication lights to signify replication

The power source and the data collection can be combined together with a V-USB connected with the Arduino and a computer. The computer can function as a high resolution screen for displaying said data. A PID system is utilized here; this system utilizes continuous control over a certain variable, which in this case is heat. It can be tuned by adjusted the P, the I, or the D, otherwise known as the proportional, integral, and derivative terms. The heating itself would happen through a resistor.

Basic circuitry diagram

A Reflection

This technology is $30K on the market, while a simple, bare bones machine can cost 1/300th of that price. It won’t function as well, nor will it be as clean cut, but it will work. For something that can diagnose disease, help sequence DNA, and recreate extinct species, the price point is unbelievably high. We need a better system, and there’s a future for this. If we can replicate DNA, we can replicate these machines for all to use,.

Resources consulted:

I’m Aniket, and I’m curious about how we can make the human experience better. If you would like to contact me, here is my Linkedin and Twitter.

I’m Aniket, and I’m interested in how we can make humans fundamentally better through better disease prevention and innovation.

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