What the heck is the polymerase chain reaction?

This molecular line dance is the most important process in genetic science

What the heck is the polymerase chain reaction?
If only the "Dance your Ph.D." competition were around for Kary Mullis [Image credit: Kevin Dooley].
By | Posted March 28, 2013
Posted in: Blogs, Ever Wondered?
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In a world without PCR, there would be no Human Genome Project. No genetic tests for disease, paternity, or crime-scene DNA. No way to tell whether the sushi you got for lunch is actually tuna. This cornerstone of modern biology copies a twisted, double-strand of DNA over and over until there is enough to sequence and analyze.

PCR may be the most important process in current science. “I use it every day,” says George Spracklin, a doctoral student in genetics at the University of Wisconsin – Madison, “I would be blind without it.” Yet most people outside of a biology lab don’t even know what the letters stand for: polymerase chain reaction.

Though the steps can seem complex, once you learn them, this molecular dance party becomes relatively simple: open up DNA into two strands, fill in the corresponding nucleotides, and voila, you have twice as much as you did before!

To visualize PCR, imagine you and a group of friends are at a large wedding reception and want to teach everybody a line dance popular in your town, called “Dance Not Alone.” You are the “P,” for polymerase, an enzyme required to assemble and repair DNA from the four chemical building blocks, adenine, thymine, cytosine, and guanine.

As with DNA, there are a few quirky rules to the dance. First, it involves two chains, made up of aunts, teenagers, cousins and grandmas. Second, like the ordained pairing of DNA’s building blocks, aunts must dance opposite teenagers and cousins opposite grandmothers. In PCR, the initial group of dancers would be similar to the DNA template, the strand of DNA being copied.

To begin, you ask the band to play something lively, but not too fast.  The dancers, arms linked in each line, move and groove, still feeling the open bar from before dinner. The band, seeing how much fun the dancers are having, decides to pick up the pace. Responding to the music, the lines soon start to drift away from each other, though still intact.

The bandleader has induced thermocycling – repeated heating and cooling – a necessary step to copy the template. DNA melts or “denatures” when heated, due to weak hydrogen bonds between the strands, leaving two single lines much like your separated dancers. You kindly ask the bandleader to slow down the music, so you can get the dancers back to doing the DNA. In the same way it would be hard to organize a line dance when people are jumping and jiving, polymerase cannot make DNA when that DNA is just going to melt apart.

But rather than herd the original strands back together, you and your friends decide to grab more aunts, teenagers, cousins and grandmas standing around on the dance floor, placing them appropriately in lines opposite the existing dancers.  Now you have twice as many dances going! The bandleader again starts playing faster. Lines drift apart. You yell at the bandleader. Your friends use more guests to fill in the empty spaces. Dance, drift, replenish, repeat.

PCR works the same way, but instead of a banquet hall full of wedding guests, it takes place in a test tube full of DNA templates and primers, polymerase, and nucleotides. Repeated thermocycling unzips each DNA molecule, allowing polymerase to grab free floating bases and rebuild the other side of the chain.

That repeated chain reaction leads to exponential growth in the number of identical DNA molecules available for testing. The scientist then has enough copies of the same DNA sequence to analyze it, which can say a great deal about the individual organism it came from. While the order of the dancers doesn’t really matter, the order of the As, Ts, Gs and Cs of DNA does, because $15 for a spicy tuna roll means you want to make sure you’re getting what you paid for.

Posted in: Blogs, Ever Wondered?

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  1. Thank you very much for the fantastic visualization of the PCR.
    I’m teaching chemistry at a school in Germany and my students always claim that they don’t understand the PCR. But with visualization of the line dance, I think they will.

    Yours sincerely

    Dr. Jochen Schenk

    Dr. Jochen Schenk, April 1, 2013 at 9:20 am
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