Why PCR, you ask… A method so popular its developer was rewarded the Noble Prize in chemistry in 1993 and that has its own song to boot?
What is it even for?
Take CSI Miami (or similar). The blond guy with the shades (ok, I just looked up his name on Wikipedia), so Horatio Caine looks down at a tiny speck of blood at the crimescene, faces the camera with a grave expression and says something profound like ‘DNA never lies.’ Well, if Horatio wants to get his bullet-proof DNA-truth he needs PCR.
Or take an afternoon talk show: the truth about the baby’s daddy is being revealed to a screaming audience. The verdict if sleezy guy A or guy B is going to be the one who tries to wiggle out of the child support payments (or who embraces the kid he never knew he had and vows to change his ways) – it’s determined using PCR.
Testing for viral infections from COVID to HIV? Often based on PCR.
And what does it do?
PCR amplifies DNA!
Many people consider DNA to be the most important molecule of life (other contenders for the throne would be RNA or proteins). Of note, some PCR techniques also measure RNA, like in the case of HIV testing, but today we’ll stick with DNA.
DNA is the long-term info storage of living organisms, handed over from parents to offspring. The molecule had a great spotlight moment when Rosalind Franklin, James Watson and Francis Crick discovered its double helix structure, in which two complimentary strands are wound around each other like a spiral staircase. This particular architecture for some reason seems to have boosted DNA’s popularity and turned it into the Rockstar among molecules. Even my grandfather who was generally more interested in history than biology, was a real fan of discussing the double helix.
And how does it do it?
In explaining what PCR does to DNA, I’m going to borrow a few terms from the world of dating (admittedly, I am much more skilled at PCR than at dating though I haven’t done either in quite some time).
To understand what happens in a PCR, the famous structure of the DNA comes back into the game. We have two complimentary strands, in which four different molecules (bases) lie opposite one another and can pair in specific ways (always two bases go together as a couple and they don’t like to couple with anyone else).
If you break up the DNA strand (which you can do by increasing the heat, STEP 1) those bases turn into lonely single molecules. Out there in the cruel world of trying to find the right match, they are looking for their complementary bases to pair with. But they can’t do it on their own. They need the help of a matchmaker. This matchmaker is an enzyme called polymerase. This is where PCR gets its P from.
So now we have our key ingredients, the DNA of interest (recently single), the new nucleotides (available candidates) and the matchmaker enzyme (OK Cupid). But the bases are still a little shy, even with the matchmaker present they need a small boost to get going on the pairing cycle (like maybe a cocktail during the first date, STEP 2). This is where the primers, short complementary DNA sequences come in and tell the matchmaking enzyme where to start its coupling business. Once those primers have done their work, the matchmaker enzyme starts adding the free nucleotides (like serial dating, STEP 3).
With the newly made DNA strands, then the same thing starts over and over until you’ve got a lot (like really a lot) DNA molecules, resulting from a lot of dates.
But wait, how does this DNA dating answer our questions, like if the suspect can be convicted as the murderer, if sleezy guy A is the baby’s daddy or if you have a COVID-19 infection?
The primers, those innocent, short DNA stretches that get the pairing going are designed in a unique way, so the matchmaker polymerase will start adding molecules at exactly the same spot on the DNA every time. And if this unique piece of DNA isn’t present (because the suspect wasn’t at the crime scene or the man is not the baby’s daddy, or you don’t have a COVID-19 infection) then there will be no amplification of the DNA.
Note that PCR itself only amplifies the DNA, the scientists still need other techniques such as gel electrophoreses or DNA sequencing to visualize the DNA and learn about its composition.
PCR has its limitations of course, the main one is that the technique is only as good as its input DNA and the primers that are being used. But if done correctly, it is a powerful technique that can answer many important DNA questions.
I hope I could convince you that PCR is one of the magical methods. And what was it with this song again? Well here it goes if you want to cheer for the method again: https://www.youtube.com/watch?v=x5yPkxCLads