[Caitlin:] Felicia, I've got the PCR samples! Now we can figure out who the murderer is. Jell-O? Really?! Is this another cooking show? Or are you just hungry this time? [Felicia:] Well, now that you mention it... I am a little hungry. [Caitlin:] Well, you're going to have to tell your stomach to wait because we've got a murder to solve. [Felicia:] I know, I know. I was waiting for you AND I'm prepared. I put this Jell-O in the fridge at the same time that I poured our agarose gel. The Jell-O is ready which means our agarose gel is ready, as well. [Caitlin:] That's pretty clever, actually. [Felicia:] Bonus. We'll have something to eat after we solve the crime. Oh. Nice sign. [Caitlin:] Making Jell-O is a lot like preparing an agarose gel. You have to add agarose to a water solution, heat it up to dissolve it, and then let it cool to set before you can use it. Right! Here is the gel. [Caitlin:] I've got the PCR samples from the blood we found at the crime scene and the reference samples from each of our subjects. [Felicia:] That's awesome! Now, we just have to put the samples in the gel and run electric current through it. [Caitlin:] The DNA will separate out by size and we'll be able to see which sample matches the perpetrator. [Felicia:] So, what are we waiting for? Let's get going with this gel electrophoresis on... [Both:] DNA Decoded! [Music] [Caitlin:] While Felicia is getting ready to electrocute her Jell-O, let me dive in to how we're going to find the killer. You may have heard that over 99 percent of the human genome is the same -- across the entire human race. So, how are we going to determine who the killer is? [Felicia:] In fact, forensic DNA analysis doesn't even look at your genes. Forensic scientists are more interested in the DNA that's in between your genes. [Caitlin:] Did you know that our DNA contains long stretches in between our genes that don't code for any proteins? For a long time, scientists weren't quite sure what their function was. They thought it was maybe junk DNA. [Felicia:] Exactly! When scientists took a closer look, they noticed that some sequences repeated themselves over and over. The repeated sequence could be anywhere from two base pairs to 100 base pairs and could be repeated anywhere from five to, I don't know, 50 times. [Caitlin:] Those regions are called Variable Tandem Repeat Regions. Let's say there's a Variable Tandem Repeat Region that is made up of the nucleotides GATA. I might have GATA repeated four times but, Felicia might have it repeated 12 times. You know, because she does tend to run on and on sometimes... [Felicia:] Hey! That's what makes me so unique. [Caitlin:] It sure does. The Variable Tandem Repeat Region's are own unique DNA fingerprint. We know where the repeating regions are in the genome. If we compare the repeating regions of the DNA at the crime scene with the DNA we collected from our suspects, we'll be able to tell who the killer is. [Felicia:] Conducting a Polymerase Chain Reaction (or PCR) to isolate the repeating regions and make copies of them, is easy-peasy. But how will we be able to tell how many times they repeat themselves? DNA's itsy-bitsy. It's not like you could just count the number of repeating base pair sequences. [Caitlin:] That's true. We may not be able to SEE the DNA, but we can use gel electrophoresis to separate out the pieces of DNA that we generated with PCR. [Felicia:] This is where this big ol' slab of agarose gel comes in. The recipe for agarose gel is similar to Jell-O, too. We measure out some agarose powder and add it to the buffer. The buffer is mostly water and some other chemicals that will let the gel conduct electricity. We bring the mixture to a boil, pour it in a mold, and let it set. The mold is just a regular dish with a nifty little comb at the top. Here's what the comb looks like. The comb has these tiny teeth which will make wells in the agarose gel once it solidifies. Okay. Now down to our crime busting business! We've extracted the DNA from the five samples from the crime scene and isolated the sections of DNA with Variable Tandem Repeat Regions. And we've made copies of these sections using PCR. Daniel here is going to help us out with our gel electrophoresis. [Caitlin:] Light up time! Before we put the samples in the wells, we add a stain that makes DNA glow when it's hit by ultraviolet light. [Daniel:] And a blue dye, so you we can keep track of what's going into each well. [Caitlin:] Agarose is a network of sugars. Think sponge toffee. There are all these channels and pores in there. It's not hard to see why agarose gel is called a molecular sieve. That's exactly how it works. We'll load each sample into an individual well. Then, the DNA fragments will race down their own lane to reach the other side of the gel. [Felicia:] When we add the samples, we want to keep track of the order. Otherwise, we finger the wrong evil doer. So, in lane one, the crime scene sample. That's the blood the killer left behind. In lane two, the sample from Bunsen, the research technician. In lane three, wearing the surly expression, Ethan Bromide. [Daniel:] In lane four, evil Dr. Blot. [Caitlin:] And in lane five, the sample from Petri Dish. [Sound of a crowd cheering and a starter's pistol going off.] [Daniel:] Larger segments of DNA have a harder time making their way through the many twists and turns inside the agarose gel than smaller segments do. [Caitlin:] Exactly! Regions with more repeats are larger. They will move through the gel more slowly, bumping into the sugars and trying to squeeze through the gaps. Regions with fewer repeats, on the other hand, are smaller and will move through the gel more quickly. [Felicia:] So, in this DNA race, we have pieces of DNA moving from one side of the gel to the other. like runners in a 100-metre race. The samples run in separate lanes and need to reach the finish line. [Daniel:] Okay, but what makes the DNA fragments run to the other side? There are no gold medals to be had at the finish line. [Felicia:] That's right. But there is electrical charge. The DNA molecule is negatively charged. We can use this to our advantage in the lab. If we apply an electric current from negative to positive direction, the negatively charged DNA will migrate (or run) towards the positive electrode. [Caitlin:] In the lab, the positive electrode is usually red, while the negative electrode is usually black. You can remember this if you remember that DNA always runs toward red. This is a screenshot from the Labster simulation. The DNA molecules are the coloured spheres. We can see the big fragments in pink and the smaller fragments in blue, running to the positive red electrode. The small blue fragments travel faster because they can get through the porous agarose gel matrix with more ease. It's time to see the race results! And here we go.... The lines show us a unique DNA fingerprint for each suspect and the sample from the crime scene. [Felicia:] So, tell us. Who should we lock up?
