Improving science literacy – part 2

PCR and gel electrophoresis

(Warning to all scientists: I’m glossing over pretty much all of the intricacies of the PCR process, so before you go telling me that you can actually make PCRs semi-quantitative or any such bullshit just sit back, take a deep breath, and realize I’m writing this for a general audience and not you.)


Have you ever seen a picture like this in CSI or some other such show and wondered what the hell it was?  Well, I’m here to tell you.  So, as they like to say, let’s begin at the beginning.

PCR stands for Polymerase Chain Reaction, and like many phrases in biology makes perfect sense if you can break down the words.
1. The suffix of -ase simply denotes an enzyme (a protein that speeds up reactions)
2. The root of the -ase word explains what the enzyme does.  In this instance it means that the enzyme creates a polymer (Polymer-ase)
3. A polymer is simply a chain of repeating units like a barrel of monkeys or, well, a chain.
4. The Chain Reaction part essentially means that this reaction happens over and over until you make it stop

So, what polymer are we creating with the PCR?  It’s a very important polymer that all of us have and hope will treat us right.  Give up guessing?  It’s DNA, and the coolest part is yet to come.

When someone takes a DNA sample the amount of DNA they actually get after purification is very, very tiny and essentially useless.  It’s useless not only because of the small amount, but also because it contains the entire genome of an animal (genome = all the DNA an animal has) and most scientists are looking for only a few select genes in that vast genome.  PCR allows us to pick and choose what genes we want to amplify, and it does so in an exponential manner (1, 2, 4, 8, 16, 32, …) because every time you make a copy of the small part of DNA you are interested in that piece than then be copied as well in the next round of amplification.  We typically copy ~30 times, so you can imagine how large a number of copies is theoretically possible (2^30), and by that time the number of amplified copies far outweighs all other pieces of DNA that might be hanging around which comes in handy in the next step.

Gel Electrophoresis

The DNA parts we created with the PCR carry an electrical charge, and this can be used to separate pieces that are of different sizes.  Essentially, you put the PCR product into a gel that contains a chemical that makes DNA glow under ultraviolet light and then run an electrical current through the gel.  The gel retards the movement of the DNA pieces in relation to their physical size.  Small pieces move faster than larger pieces.  Then you shine a UV light on the gel and take a picture of it and you get the above image with a bunch of horizontal bands.  Each band is a bunch of identical pieces of DNA of a particular size (the closer to the bottom of the picture the smaller the piece of DNA).  Cool, huh?

Real Life Uses
Paternity tests, genetic screening, and detection of certain diseases are some of the common ways people are directly affected by this amazing technology.  Say you go in to be screened for a gene that is linked to aggressive cancer; they take your DNA, mix it with a few specific chemicals, do the PCR, use the PCR product in a gel electrophoresis unit, and then you get a picture.  If there is a band in the right spot then you have the gene, but if there is no band then you don’t (if there is no gene to amplify then there won’t be a band of DNA in the gel – it will be completely blank).

And that’s how science touches the lives of just about everyone in America.  Ain’t it amazing?



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Filed under Those Other Sciences

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