PCR (no, not Ponies Conducting Reseach)

You’ve probably heard a bit about ancient DNA – it’s been in the news a lot recently.

DNA (or deoxyribonucleic acid) is a molecule that encodes the genetic instructions used in the development and function of all known living organisms (including you and me). Ancient DNA is the same as modern DNA, it’s just older (usually a lot older).

It’s been used to identify Richard III by linking the skeleton from the car park to his living relatives (more on him in the next blogpost). It’s shown that the strains of plague bacteria responsible for the medieval and the earlier Roman epidemics were distinct. And it’s even revealed that some Neanderthals probably had red hair.

Which is amazing. But have you ever wondered exactly how researchers actually get this ancient DNA? Well wonder no more.

It all starts when researchers extract a DNA sample – usually from a bone or tooth, which could be hundreds or thousands of years old.

Or, perhaps I should say more accurately, researchers extract a sample that has lots DNA fragments in it… oh and it will also almost certainly include DNA fragments from contaminants – like from the soil or even the researchers themselves.

Now, you can’t just look at the fragments and find the ones you’re interested in studying, because there will only be a few of them. So you need to amplify them – or make copies, to make them more obvious and to give you more to work with in your research.

Enter PCR. Polymerase chain reaction. (See, not ponies conducting research.)

Now, most of us will recognise the DNA’s distinctive double helix. This is made up of two single strands of DNA, with the nucleotides, or bases: guanine, thymine, cytosine, and andesine (or: G, T, C, and A), matching up in the middle – A and G matching up together and T and C matching up and annealing – or attaching together.

DNA is absolutely not made of cadboard and colourful duct tap, but let's pretend!

DNA is absolutely not made of cardboard and colourful duct tap, but let’s pretend, eh?

So, you pop your sample – which remember includes all of the DNA fragments still – into a test tube along with a solution that contains primers,

Ooh, shiny primer.

free nucleotides (that’s the Gs, Ts, Cs, and As),

“We’re free spirits*!” *nucleotides

and an enzyme called DNA polymerase.

Sadly, it does not actually look like Mushroom from Super Mario Kart.

Now the primers are a very important part of the solution. These are small segments of a single strand of DNA, which are chosen by researchers because their nucleotides will match up to a unique section of the DNA they are interested in copying.

Once you’ve got your test tube with everything you need in it for PCR:

Now pretend that my floor is the inside of a test tube (which in the past has been played by the part of a purple bucket).

Now pretend that my floor is the inside of a test tube (which in the past has been played by the part of a purple bucket).

– you pop it into a machine called a thermo cycler, which will begin the process by heating up the DNA fragments (to about 94-98°C) so that they denature, or separate into two single-strands of DNA.

The sample is then cooled (to 50-65°C), and those primers will seek out the unique sections of the single-strands that match up to their nucleotides and anneal – or attach to them.

This tells the DNA polymerase where to start synthesising, or building, by activating those free nucleotides into attaching to their matching pair on the single strands – so they fill in the blanks themselves, in a chain reaction (usually at about 70-80°C).

A little bit like this:

This process results in the duplication of the original DNA, with each copy containing one old (black tape) and one new strand (silver tape) of DNA! You may have noticed that the animation above only shows one, this is because the other half still looks like cardboard – instead of cardboard covered in colourful duct tape – but just imagine that this process has happened to the other strand as well, as it would in reality). Then each of these strands can be used to create two new copies, and so on, and so forth.

The cycle of separating and building new DNA is repeated as many as 20 to 40 times, leading to more than one billion exact copies of the original DNA segment… in just a few hours.

And just like that (with a few caveats) you’ve got enough of the ancient DNA you’re interested in studying, so now you can tell us all about everything from disease mutations to human origins, or even what woolly mammoths ate.

Not bad for a scientific method developed before Back to the Future was released, eh?

If you’re interested in listening to a great description of the PCR process, check out this recent Naked Scientists podcast. In fact, just listen to the entire podcast, because it’s great!

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2 responses to “PCR (no, not Ponies Conducting Reseach)

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