How to Copy DNA: The Invention of the Polymerase Chain Reaction

Jan 11, 2018

By Matt Niederhuber

There’s a good chance you’ve heard about DNA testing before, probably on a crime TV show or on the news. Sometimes, DNA testing is how the police identify suspects, but it has also helped prove the innocence of many people who have been falsely imprisoned.

I bring up DNA testing because I want to tell you about the technology that makes it possible. It’s called the Polymerase Chain Reaction, or just PCR for short. From detecting disease, scientific research, and even genetic engineering, PCR is one of the fundamental tools that scientists use in the lab. The purpose of PCR is to make many copies of a DNA sequence of your choosing.

The basic idea of DNA testing is that even though we all have very similar sequences of DNA in our cells (around 99.5% of my DNA is the same as yours) we also have unique variations that can be used to identify an individual. PCR makes billions of copies of the DNA sequence that you want to look at, making it possible to find those variations. Without making lots of copies you couldn’t detect the sequence you were interested in, otherwise it would be like trying to hear a single instrument in a very large orchestra.

So, what exactly does the Polymerase Chain Reaction do? “Polymerase” is a protein that makes copies of DNA, and cells use polymerase to copy DNA when they divide. “Chain reaction” describes how PCR is an exponential reaction. Each time polymerase makes a copy, the number of copies doubles. If you start with 2 identical DNA sequences and then copy them you make 4 sequences. Copy those to make 8, then 16, then 32, and so on. After 35 rounds of making copies, PCR produces around 34 billion pieces of the target DNA.

The steps of PCR. After every round of amplification, twice as many pieces of DNA are made. Image credit: Matt Niederhuber. Image based on figure from Wikimedia commons.

These days, we have instruments that run PCR for us. All we have to do is mix  the reaction ingredients and then pop it in to the machine called a thermocycler. Back when PCR was first invented in 1985, it was a huge pain in the neck. Every time you wanted to copy DNA,  it had to be heated up, destroying any polymerase in the test tube.  Then, after each round of heating, fresh polymerase had to be added.

The big discovery that made modern PCR possible came from an unexpected  place: the hot springs at Yellowstone National Park. Scientists found a special type of bacteria that happily live in these 170oF hot springs. These  are called thermophiles because they love (-phile) the heat (thermo-), and they have a lot of special abilities that make it possible for them to live in these super hot places.

Researchers that were studying one thermophile in particular, Thermus aquaticus, discovered that the polymerase it used to replicate its DNA wasn’t destroyed at high temperatures like the polymerase our cells make. The scientists working on the PCR technology realized that if they took advantage of this polymerase they might not have to add more of it after every round of copying.,_Yellowstone_National_Park_(3646969937).jpg

Thermus aquaticus were found in the hot springs of Yellowstone National Park. Scientists isolated polymerase, the enzyme that copies DNA, from these bacteria for use in PCR. Image credits: Yellowstone Grand Prismatic Spring, Thermus aquaticus, T. aquaticus polymerase modelled in PyMol.

They were right. Using the polymerase from Thermus aquaticus made it possible to run PCR automatically, without stopping and adding more polymerase to the reaction. This breakthrough was a big reason why Kary Mullis, the inventor of PCR, won the Nobel Prize in 1993.

It was this creative leap of using polymerase from a thermophilic bacteria that  made it possible for PCR to become a common and inexpensive  tool, both in science and other fields  like law enforcement. It just goes to show you that it’s sometimes the weirdest ideas that make for the biggest discoveries.


Edited by Mike Pablo, Jennifer Schiller, and Christina Marvin