Gel Electrophoresis

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When I was a young kid I was really interested in genetics. Well I didn't really understand genetics. I kind of thought that when two organisms had a baby, the baby was just this blend of the two.

Yeah that's a misconception. But I really saw genetics in action with my guppies. Guppies are very easy freshwater fish to keep in an aquarium, but they have two things that I think are especially cool.

They have live birth which means there are no eggs like many other fish, and second, they have a lot of babies. They also eat their babies, but I don't think that's especially cool so as you can see, it's not part of my cool fact list. Anyway when my surviving baby Guppies grew up they would have all kinds of cool traits.

These traits were carried by their DNA, their genetic material, which is found in their body cells. But sometimes I would forget which mother was the mother of the baby guppy, because there were several mother fish in the tank, and I wanted to keep track of inheritance in my guppy notebook. So what would have been very cool to have at that time?

Some biotechnology! Biotechnology is the merge of biology and tech, and it's constantly changing! It includes topics such as PCR, cloning, and genetic engineering.

It's also an awesome field. We're gonna talk about one of the bio technologies that could have, well potentially, helped me determine the genetic relationships of my guppies. .

. if you know as a young kid I had access to it. Although it's becoming way more common in classrooms now.

And that biotechnology is gel electrophoresis! Gel electrophoresis can be used to separate molecules based on how big they are (their size) and it's especially useful with DNA. Let's look at DNA real quick.

So here is a guppy cell. Here's the nucleus in the guppy cell. Here's the DNA in the nucleus of the guppy cell, and if you were to zoom into the DNA, here is a nucleotide which is a building block of DNA.

See those phosphates in the nucleotides? They're a bit negative. Well they contribute a negative charge anyway to the DNA.

So if we look at this whole DNA here it gives that DNA a negative charge. That's a big deal, because gel electrophoresis which again separates molecules based on size relies on the fact that DNA molecules have a negative charge. Okay, here's a gel electrophoresis machine.

The point of the machine is to be able to have an electrical charge running through a gel so here's the gel typically made of agarose. Agarose is a polysaccharide polymer, which if you remember from our biomolecule video, polysaccharides are carbohydrates. Yeah, usually agarose comes from seaweed.

The agarose gel itself lets the DNA molecules travel within it. One end of the gel has these holes called wells. The wells are where the DNA is placed into The area of the gel where the wells are is negatively charged, and the area of the gel here is positively charged.

So guess where the DNA will travel towards? Well since it's negatively charged, it's going to travel to the positive side. So typically when you're analyzing DNA in electrophoresis you use these restriction enzymes to cut the DNA up into tiny pieces.

Restriction enzymes have the ability to cut up DNA in very specific areas, often related to the specific DNA bases, making restriction enzymes very useful in biotechnology. So if I had baby guppy DNA and adult mother guppy DNA, and I want to compare them, then I would want to use the same types of restriction enzymes in both DNA samples. If I used the same type of restriction enzyme, it should be cutting the DNA at the same identification points in the DNA samples.

However, unless the mother and baby guppy are clones (and they're not), those pieces that result after the restriction enzyme is done with them may be differently sized because the DNA of the baby and mother guppy had some differences in the sequence of their DNA bases. So the DNA samples both are cut into multiple pieces by the same type of restriction enzyme and then those samples are loaded into the gel sample1 and sample2. If we turn on the machine and let the DNA run through the gel, the DNA moves towards the positive side.

But some pieces of that cut up DNA will move faster or slower than other pieces. Longer DNA pieces tend to have a higher molecular weight and they take more time to make it across the gel when you compare it to shorter DNA pieces which move at a faster rate. So what you end up with is that these DNA fragments spread out with the longer pieces closer to the wells and the shorter pieces closer to this opposite side of the gel.

These are called DNA bands, but to see them, you usually need to stain the gel itself and view it under a UV light. Now let's compare the DNA bands in this hypothetical simplified guppy situation. The bands aren't going to be identical, because these fish are not clones, but I can compare how similar the bands are and compare that to other mother guppy samples to look for relationships.

Let's say that we have three mother guppy samples to view and these are the only possible mothers from the fish tank. Which one appears to be the most related to the offspring in this case and has a high likelihood of being the mother? Well this one.

But we can't be 100% sure with this, It would be helpful for me to know the father guppy sample too because this will give you more insight. But if these are the only fish in the tank, it's a very high likelihood with this case. Also, you can use something called a DNA ladder!

You can buy them from various science material distributors, but a DNA ladder is not what it sounds like. It's basically a sample that has known fragment sizes so if you run it in the electrophoresis machine, you already know the fragment lengths. Let's say this DNA ladder only had three bands, which is not usually the case.

Since it's a DNA ladder, the base pair lengths are known. They are 500 base pairs, 1,000 base pairs, and 1,500 base pairs. Think fora minute.

. . where would they fit in?

It would look like this! You can use this now as a reference to give estimates of how large the other fragments are when they're run alongside it, and if you want to be closer to the value, you can use a stand my love graph something to look up. So why do we care about gel electrophoresis?

It's not likely I'll be actually using this with my guppies anyway, right? Well perhaps. But gel electrophoresis is often a step used in determining relatedness with different species, which help scientists better classify organisms!

It's also used as part of DNA fingerprinting. DNA fingerprinting is a way that one can identify someone's DNA which can be very helpful if you're trying to solve a mystery involving a crime scene. If you have a DNA sample from a crime scene, you can go through the steps of gel electrophoresis to compare it to the suspect DNA to see the likelihood of a match.

In fact, you can take the results from gel electrophoresis and isolate genes of interest by something called southern blotting. Definitely something to look up if you're curious. Gel electrophoresis is one of many awesome tools in biotechnology.

Well. . .

that's it for the amoeba sisters, and we remind you to stay curious.