Polymerase chain reaction (PCR) | Biomolecules | MCAT | Khan Academy

I'm here with Emily, our biology content fellow, to talk about PCR or polymerase chain reaction, which you've actually done a lot of.

Why have you done PCR?

PCR was kind of the mainstay of my graduate project, where I built all sorts of different recombinant DNA molecules and used them to learn things about plants.

And so what does PCR in particular do?

PCR basically makes you a lot of copies of a particular fragment of DNA that you're interested in.

And why would you need to make a lot of copies of a particular fragment of DNA?

You might want to be making lots of copies so that you can clone it into a plasmid and then do some other experiments with it; that's a big use.

So when we talked about cloning and we're talking about sticking a fragment of DNA inside of a plasmid, it's not like you're just taking one fragment into one plasmid; you're doing that with many, so you need a lot of fragments of DNA.

Exactly! That is exactly it. You might start with a very small sample of DNA, and so you just really need to.

Where else would you have to do PCR?

PCR is used a lot in forensics. It's also used a lot in medical diagnostics. So this could actually be your DNA that was being checked to see if you have a gene that would predispose you to a particular condition.

All sorts of really practical applications because it's hard to identify just one fragment of that gene. So you'd want to make copies, or as they say, amplify it so that you could run it in gels and stuff and see how all of those molecules, how big they are or something like that.

Exactly! If you were just looking in your DNA pulled out of your cell, that would be a needle in a haystack. So this is how you can really zoom in and look at just the thing you need to see.

Okay, so you've drawn some diagrams here, and I actually have never done a PCR, but you have.

So I'm going to tell you how I understand it happening, and then you tell me if this makes sense.

So what you drew over here—this is double-stranded DNA, you know. This could have been from a sample of someone's hair or whatever else, and let's say we want to replicate or make many, many copies of a fragment of this.

Let's say the fragment that we really care about is the fragment roughly from there to there. This part is what we want to make. We want to make multiple copies of.

And so this first step: denaturation.

Denaturation! I have trouble pronouncing this; it's a weird word.

It's a weird word. You have 96 degrees Celsius, so this is almost at the boiling point. It's quite hot, and that separates the two strands precisely.

And so once they're separated, then you can cool things down; although this still isn't that cool—55 degrees Celsius would be very uncomfortable—but you would cool it down to this, and then these primers show up.

And so you know one thing to remind ourselves is this process is happening inside of a test tube or in a big solution.

So you heat it up, the DNA, the two strands separate, and do you just have this primer lying around?

The primer is something that you've ordered from a company, and you've ordered a lot of it. So you put in a ton of primer in your reaction so that there's a really good chance that when you get to this step here called annealing, that a primer is going to bind to many of your pieces of DNA.

So this is our solution. Is this all happening in water?

Water with some salts and stuff floating around.

Yeah, okay! So we have our solution right over here. You'd put whatever your initial DNA sample is in there, and once again, it's a very small amount. You'd put a lot of that primer, so you'd want to put that in a lot of surplus.

So let me do that in a magenta color. You obviously wouldn't see it in real life; it would just all dissolve. It would just look like a drop of liquid.

It would look like... but for visualization, you put a lot of primer. So you heat it up, the DNA strands separate, and then when you cool it back down, this primer is going to be specific to the ends of the region that you want to copy.

Exactly! And so when you go to the—when you order online or wherever that you want a certain primer, you're going to pick the sequence of that primer to be specific to the regions you want to copy.

Exactly! That's super important.

Okay, and so when you cool it back down, the primer attaches, and then you heat it back up—not quite to the 96 degrees Celsius, but to the 72 degrees Celsius—where you extend those.

And I'm assuming since it's called polymerase chain reaction, that this is where the polymerase is involved?

That is exactly where the polymerase comes in!

So the polymerase—the polymerase is what is actually extending this.

And is it any type of polymerase enzyme? Could I just take, like, you know, the polymerase for my cells and throw it in there?

So you actually need a special polymerase because you need one that is going to be pretty heat resistant.

So as you were mentioning, even the cool step of this process is not something that your body would want to be hanging out in. So the polymerase is actually from a really heat-tolerant microorganism, and what is that?

It's called Taq polymerase, Thermophilus aquaticus, I think makes quite a mouthful, and they found it at heated vents—this organism that is able to stand these high temperatures.

But that, I guess, leads to another question. Why? Well, why do you have to heat it up to begin with?

I guess just to separate the two strands. That's really the key reason; you just have to get them apart. You don't have an enzyme to do it the way you might in a cell, so heat does the trick.

Okay, so I get it. So this is one step I'm guessing I’m getting at least the polymerase part of the PCR, where you heat it up, the strands separate, then you have all of this extra primer there—the primer.

Because there's so much primer, the primer is much more likely to bind to, at least at this part of the sequence, than for these two strands to get back together at this point.

And then you have the polymerase—the Taq polymerase in particular—and you would have added that at the beginning.

You know the Taq polymerase, I guess I'll put it in this—I'll do it in a yellow color—so you would already, you would also put all that Taq polymerase in there.

And once again, you know, these things aren't robots; they don't know exactly what they need to do. They just bump into things in the right way and react in the right way.

And you also have to add a bunch of nucleotides!

Yes, absolutely! Your reaction is not going to work if you forget the nucleotides.

So the Taq polymerase, when you heat it back up again after the primers have been attached, is going to start adding all of these nucleotides.

And what do you just wait a certain amount of time? Will it just keep going on forever?

It'll keep going on for a while. Usually, you do pick the length of that step to match how much time you expect the polymerase to need to complete your fragment on, but it will kind of stop. Either it'll fall off or it'll stop when you go on to the next step.

Okay, so this—I get this! So far, so far, we have after one cycle, let me—what you’ve written here—after one cycle, we would have doubled at least that part, that part of the sequence that we care about, although we might have even— we might have copied even beyond that sequence.

So where does the chain reaction come into this?

So I guess you can interpret chain reaction in two ways. One is that's sort of what the polymerase does; it adds things to make a chain. But there's actually even more of a chain reaction dimension here, and that's that we're actually getting this kind of exponential process going on.

So you do it one cycle; you get to this situation right here. You heat it up, the strands separate, you cool it down, the primers attach, you heat it up again, the Taq polymerase does its job, and like all polymerases, it goes from the five prime to the three prime direction we talked about in that application.

So now you have two strands, but now since all that stuff is in that solution, you can just keep— you can heat it up again. Now each of these two strands can turn into—or these two double strands can now turn into four single strands.

Then you can cool it down again; now they get primers attached to them, and they're still the same primer because we still care about the same sequence.

And then that can key—and so now you go from one to two to four, and so you keep repeating this.

And so how many times would it be typical for you to repeat this cycle?

So like 35 might be a pretty typical number of cycles to do; it depends a little on what you're doing, but you're going to do it a lot of times.

And so if you do this 35 times, I mean, each time you're multiplying by two, so it will be two to the 35th power, which is, well, over a billion times.

So, and how long would that take? You've done this before.

It depends on the length of your fragment, but usually like two to three hours.

So in two to three hours, you can start with one fragment and get into the billions if it's perfectly efficient.

Which I wish it always were, but you usually get quite a few pieces made.

And one thing that I've always wondered when I first learned about this, and I'd like to go to a lab and do this with you, is—okay, I get that you have your primer and then the polymerase is just going to extend it like that.

But I was like, well, it's, you know, it's going to be—how does it know where to stop?

And you explained, well, on that first pass, it might not know where to stop, but then when you start going in the other direction, it's going to.

So over here, when it goes in the other direction, it's going to hit a—it's going to hit a—it’s not going to have anything else to copy!

Exactly! And so then you're—so most of the billions of molecules that you produce are going to be both ends, kind of a nice clean cut.

The vast, vast majority!

Exactly! Fascinating!