Southern blot | Biomolecules | MCAT | Khan Academy

So in this video, I'm going to be talking about something known as a southern blot. So a southern blot basically allows you to visualize a specific piece of DNA that you're interested in. So let's imagine that we have a cup, and it's filled with DNA. So it's got just a whole bunch of DNA inside. And there's just lots and lots of this DNA, and let's imagine that I'm specifically interested in one gene. Let's imagine that I'm interested in gene A. And I want to see if gene A is inside of this cup that fits inside of this long piece of DNA. Now, in order to figure out whether or not gene A is inside this cup, basically we have to do this process known as a southern blot. And we'll break it up into a couple of different steps. So step one, what we're going to do is we're going to take this DNA, and we're going to cleave it. So take the DNA and cleave it. So let me draw that out. So we're going to take this big old strand. We're going to remove it outside of the cup over here. We've got this big strand, and we're going to cut it up. We're going to expose it to enzymes that will basically cleave the DNA in a whole bunch of different parts. And that'll result in lots of these smaller pieces of DNA. And so that's basically the first step. So we've got a bunch of small little pieces of DNA. Now, step two, what do we do? Well, what we're going to do is we're going to take all these tiny little DNA fragments, and we're going to run them on the gel. So specifically, we're going to do a gel electrophoresis on these DNA fragments. And I made a video on gel electrophoresis, so if you want to refresh, you can watch that video. But basically, the gel electrophoresis will help us separate these DNA fragments based on size and based on charge. So let's just diagram that out. So we're going to take these DNA fragments, and we're going to run them on a gel. So let's imagine that this is the gel, and we add the DNA fragments to different wells. So the fragments are going to move down the gel, and they're going to basically be separated based on size and based on charge. So we're going to have these fragments separated, like so. So now we've got this gel, and we've got the DNA fragments separated by size on this gel. So the next step, step number three, is basically we're going to take this gel, and we're going to transfer it to a filter. So transfer the gel onto a filter. And what the filter will basically allow us to do is it will allow us to visualize, because this gel is very flimsy, so we want to transfer it onto a filter. So what we'll do is we'll take a filter that's basically the same size as the gel, and we're going to basically just put it right on top of the gel for a little bit, and the fragments will basically transfer onto the filter. So now we're going to have a filter with these fragments, and the filter's a lot sturdier than the gel. So this is the filter, and I'll just write that down over here, and this over here is the gel. Okay, so the next step, step number four, is we're going to take the filter, and we're going to expose it to a radio-labeled piece of DNA. So expose to radio-labeled DNA. Now this radio-labeled DNA is going to be the complement to our gene of interest. So we're interested in finding out if DNA is present in this massive DNA over here. So what we do is we're going to take the complementary sequence to DNA, and radio-label it, and expose it to this filter. So let's imagine that the radio-labeled piece of DNA is this pink piece of DNA, and let's imagine that we do have gene A. So let's imagine that this piece of this DNA fragment was actually gene A, our gene of interest. So what's going to happen is when we expose the radio-labeled DNA to this filter paper, it's going to anneal to our gene of interest. So we're going to have this radio-labeled piece of DNA stuck to this DNA fragment, which is its complement. So in order to visualize it, in order to visualize this radio-labeled piece of DNA, we have to do the fifth and final step, which is expose the filter to an X-ray film in order to visualize the radio-labeled probe. So expose to X-ray. And the X-ray basically, it'll shoot a bunch of X-rays, and since this piece of DNA is radio-labeled, it will pop up on the X-ray film. So we're going to have a film, and we'll draw that film over here. So we'll have this film. And basically, the only thing that'll pop up is this fragment over here. And that fragment will have a control, and we'll be able to say, okay, well, since we have this fragment, it's basically the radio-labeled piece of DNA. And since we see the radio-labeled DNA, it means that it had bound, it was bound to this gene A, which means that gene A was in this cup of DNA.