Using Bioinformatics to Study Evolution: Animating PCR

i-6d3784373c1ae06545f859a0aec5dcd9-dnai.gifIf we asked any biologist to pick the five most important techniques in biology, that list would certainly include PCR. 

PCR stands for Polymerase Chain Reaction. It's used everywhere. We use it to amplify DNA for cloning, we use it for diagnostic tests, for DNA sequencing, for identifying pathogens, for identifying our long-lost relatives (and sometimes parents), and in forensics.  If there's a technique that involves DNA, PCR is probably involved somewhere, too.

Since PCR is such an important technique, and we're going to be using PCR in our course, it's worth checking out a few animations to get in the right state of mind.

Like so many things, you have to follow a bit of a convoluted path to get to the right place.

Start out by going here. When you get there, follow the path that you see below to find two PCR animations.

i-75f18bb8727d7bd2d3ca5ef7cab4daf9-path_to_PCR_animation.gif

Both animations illustrate the steps in PCR. The first animation (Making many copies of DNA) is interactive. There is one confusing step though, after you click the link, you will reach this page:

i-c4f76398e2a5b8446f8a6affbd2dfe96-2d_animation.gif

I found that it's not obvious to all students that you need to click the word "Amplification". (I guess the dnai designers should read one of my favorite "Joel on Software" posts on Designing for people who have better things to do with their lives.)

Anyway, back to the animations. The first animation is very nice for students because, once they've solved the puzzle of starting it, they must click different buttons like "Denature DNA" to see what happens when DNA is denatured. The rest of the tutorial continues in the same vein through five cycles of PCR until you've amplified a specific region of DNA. There's even a graph to show how the number of molecules of a DNA fragment increase with each cycle.

It's wonderful.

The second animation was created, so I'm told. by the people who did some of the work for the Harry Potter movies. It shows. This animation wins my vote for the one with the "Wow" factor.

The downside is that students find the second animation so convincing that they think that they're looking at the real thing.

Still, I enjoy it. Just be sure to hit the Mute key before you start, since there's no option to turn off the sound.

And make your students repeat this phrase: "it's only a movie, it's only a movie"

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That is so cool. I'll have to show this to my girlfriend so she can finally figure out what the hell I do all day.

In this study, what evolved into what?

By James Collins (not verified) on 22 Jun 2007 #permalink

Thanks bdf!

James: I don't that we're likely to see anything evolve into something new in this study - or to phrase it like a biologist, we're not likely to see new species emerge in this study.

However, there are some co-evolution studies where people do see evidence that new species are starting to appear. I have a friend who's found this happening with monkeyflowers and it's pretty amazing. I'll write more about it later.

Assignment 1: WIP1

WIP1 codes for wound induced protein in corn Zea mays. WIP1 is homologous to Bowman-Birk proteinase inhibitor. It is a serpin-like protein. Serpin1 of Arabidopsis thaliana is a suicide inhibitor for metacaspase 9.

References:Eckelkamp C, Ehmann B, Schopfer P. 1993. Wound-induced systemic accumulation of a transcript coding for a Bowman-Birk trypsin inhibitor-related protein in maize (Zea mays L.) seedlings. FEBS Lett. 1993 May 24;323(1-2):73-6.Rohrmeier T, Lehle L. 1993. WIP1, a wound-inducible gene from maize with homology to Bowman-Birk proteinase inhibitors. Plant Mol Biol. 1993 Aug;22(5):783-92.Vercammen D, Belenghi B, van de Cotte B, Beunens T, Gavigan JA, De Rycke R, Brackenier A, Inz� D, Harris JL, Van Breusegem F. 2006. Serpin1 of Arabidopsis thaliana is a suicide inhibitor for metacaspase 9. J Mol Biol. 2006 Dec 8;364(4):625-36.

By Antonieto Tan (not verified) on 24 Jun 2007 #permalink

Ops, sorry. I the posted "assignment 1: WIP1" in the wrong blog. Please delete. Thanks.

By Antonieto Tan (not verified) on 24 Jun 2007 #permalink

"..Start out by going here. When you get there..."

I clicked on "here" and then clicked again but I did not get "there", all I got was an empty page?!

Very much interested to see the animations - I'm looking for some new ones to show to visitors to our lab (we are doing PCR based testing..)

Will appreciate your response,
Beni

By Beni Kaufman (not verified) on 26 Jun 2007 #permalink

Hmmm, here are some reasons that you might see a blank web page:

1. Their server can't handle the traffic.

2. The web site is all done in FLASH and FLASH is SLOW. You have to have the right version of FLASH installed on your computer.

Three possible solutions are:

1. Go to the main dnai entry page: www.dnai.org They might tell you which version of FLASH you need to download. If not, go to www.adobe.com and get the latest version of FLASH from there.

2. See if entering from the main page will work better. Go to www.dnai.org, and click the word "Manipulation" in the top menu bar. Then follow my directions above.

3. If all else fails, you can buy the DVD from Cold Spring Harbor Laboratory. Some of the stuff is kind of silly, but there are gems, too.

When I first saw these sorts of animations, or even paper diagrams of the PCR process, what actually confused me was the fact that in order to simplify it they left out one crucial element. That is the fact that the reaction is essentially one of extending DNA primers and as such the initial reaction contains a huge excess of primers. This fact is hidden in most diagrams but I think doing so obscures a key driving force of the reaction - the fact that so many primers are available for extension.