Explainer: How PCR works | Science News for Students

Explainer: How PCR works

What a photocopier does for images and text on paper, PCR does for snippets of DNA
Jan 30, 2017 — 7:09 am EST

A researcher at the National Cancer Institute adds materials to a test tube before copying some segment of DNA using the polymerase chain reaction, or PCR.

Daniel Sone/NCI

Copy machines are handy in schools and offices because they can quickly duplicate pages from all types of sources. Similarly, biologists often need to make many, many copies of genetic material. They use a technology called PCR. It’s short for polymerase (Puh-LIM-er-ase) chain reaction. Within just a few hours, this process can make a billion or more copies.

The process starts with DNA, or deoxyribonucleic (Dee-OX-ee-ry-boh-nu-KLAY-ik) acid. It’s a playbook with instructions that tell each living cell what to do.

To understand how PCR works, it helps to understand the structure of DNA and its building blocks.

Each DNA molecule is shaped like a twisted ladder. Each rung of that ladder is made of two linked chemicals, known as nucleotides. Scientists tend to refer to each nucleotide as A, T, C or G. These letters stand for adenine (AD-uh-neen), thymine (THY-meen), cytosine (CY-toh-zeen) and guanine (GUAH-neen).

One end of each nucleotide holds onto an outside strand — or edge — of the ladder. The other end of the nucleotide will pair up with a nucleotide holding onto the ladder’s other outside strand. The nucleotides are picky about who they link up with. All A’s, for instance, must pair with T’s. C’s will pair only with G’s. Each letter is therefore the complement of the other in its pair. Cells use this picky pairing pattern to make an exact copy of their DNA when they divide and reproduce.

That pattern also helps biologists copy DNA in the lab. And they might want to copy only part of the DNA in a sample. Scientists can tailor which bit they copy using PCR. Here’s how they do it.

Story continues below image.

double helix
An artist’s depiction of part of a DNA molecule. The nucleotides show up as colored half-rungs of the twisted-ladder, with A in green, T in blue, C in orange and G in yellow. Each nucleotide attaches to an outside strand of the molecule, and to its complement nucleotide. As a DNA molecule gets ready to reproduce, it splits down the middle of the ladder, with each nucleotide letting go of its complement.
colematt / iStockphoto

Heat, cool and repeat

Step one: Insert DNA into a test tube. Add in short strings of other nucleotides, known as primers. Scientists choose a primer that will pair with — or complement — a specific series of nucleotides at the end of the DNA bit they want to find and copy. For instance, a string of A, T and C will only pair with a T, C and G. Each such series of nucleotides is known as a genetic sequence. Scientists also throw into the mix a few other ingredients, including single nucleotides, the building blocks needed to make more DNA.

Now place the test tube into a machine that heats and cools these test tubes over and over again.

A normal piece of DNA is described as double-stranded. But before it prepares to reproduce itself, DNA will split down the middle of the ladder. Now the rungs separate in half, with each nucleotide remaining with its adjacent strand. This is known as single-stranded DNA.

With PCR technology, after the sample cools down again, the primers seek out and bind to the sequences they complement. Single nucleotides in the mix then pair up with the rest of the open nucleotides along the targeted single strand portion of DNA. In this way, each original bit of target DNA becomes two new, identical ones.

Each time the heating and cooling cycle repeats, it’s like pressing “start” on a copy machine. The primers and extra nucleotides duplicate the selected portion of DNA again. PCR’s heating and cooling cycles repeat over and over and over.

With each cycle, the number of target DNA pieces doubles. In just a few hours, there can be a billion or more copies.

PCR acts like a genetic microphone

sample rack
This researcher at the National Cancer Institute is preparing a rack of genetic samples and primers for the polymerase chain reaction, or PCR.
Daniel Sone, NCI

Scientists describe this copying as amplifying the DNA. And that’s the real value of PCR. Think about walking into a crowded cafeteria. Your friend is sitting somewhere inside. If your friend saw you and said your name, you might not hear it above all the other students talking. But suppose the room had a microphone and sound system. If your friend announced your name over the mike, that voice would drown out all the rest. That’s because the sound system would have amplified your friend’s voice.

Similarly, after PCR has copied a selected bit of DNA in some sample, those over-represented copies will drown out everything else. The process will have copied the target snippets of DNA so many times that soon they vastly outnumber all of the rest of the genetic material. It’s like trying to pick out just the red M&Ms from a big bin. Picking out individual candies would take a really long time. But suppose you could double the red M&Ms over and over. Eventually, nearly every handful would contain just what you wanted. 

Scientists use PCR for many types of work. For instance, scientists might want to see whether someone has a certain gene variation, or mutation. That altered gene might signal the person has a higher risk for a certain disease. PCR also can be used to amplify tiny bits of DNA from a crime scene. That lets forensic scientists work with the evidence and match it to other samples, such as DNA from a suspect. Environmental scientists might use PCR to see if any of the DNA taken from a river matches a particular species of fish. And the list goes on.

All in all, PCR is a really handy tool for genetics work. And who knows? Maybe one day you’ll find yet another use for this DNA copying machine.

Power Words

(more about Power Words)

amplify     To increase in number, volume or other measure of responsiveness.

cell   The smallest structural and functional unit of an organism. Typically too small to see with the naked eye, it consists of watery fluid surrounded by a membrane or wall. Animals are made of anywhere from thousands to trillions of cells, depending on their size. Some organisms, such as yeasts, molds, bacteria and some algae, are composed of only one cell.

chemical      A substance formed from two or more atoms that unite (become bonded together) in a fixed proportion and structure. For example, water is a chemical made of two hydrogen atoms bonded to one oxygen atom. Its chemical symbol is H2O. Chemical can also be an adjective that describes properties of materials that are the result of various reactions between different compounds.

complement   To match or fit with something else to complete it. In genetics, a series of nucleotides that pairs exactly with another sequence of DNA or RNA is called the complement of that sequence.

DNA  (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.

DNA sequencing    The process of determining the exact order of the paired building blocks — called nucleotides — that form each rung of a ladder-like strand of DNA. There are only four nucleotides: adenine, cytosine, guanine and thymine (which are abbreviated A, C, G and T). And adenine always pairs up with thymine; cytosine always pairs with guanine.

environmental science   The study of ecosystems to help identify environmental problems and possible solutions. Environmental science can bring together many fields including physics, chemistry, biology and oceanography to understand how ecosystems function and how humans can coexist with them in harmony. People who work in this field are known as environmental scientists.

forensics    The use of science and technology to investigate and solve crimes.

gene   (adj. genetic)  A segment of DNA that codes, or holds instructions, for producing a protein. Offspring inherit genes from their parents. Genes influence how an organism looks and behaves.

genetic sequence   A string of DNA bases, or nucleotides, that provide instructions for building molecules in a cell. They are represented by the letters A,C,T and G.

mutation  Some change that occurs to a gene in an organism’s DNA. Some mutations occur naturally. Others can be triggered by outside factors, such as pollution, radiation, medicines or something in the diet. A gene with this change is described as a mutant.

nucleotides    The four chemicals that, like rungs on a ladder, link up the two strands that make up DNA. They are: A (adenine), T (thymine), C (cytosine) and G (guanine). A links with T, and C links with G, to form DNA. In RNA, uracil takes the place of thymine.

polymerase chain reaction (PCR)    A biochemical process that repeatedly copies a particular sequence of DNA. A related, but somewhat different technique, copies genes expressed by the DNA in a cell. This technique is called reverse transcriptase PCR. Like regular PCR, it copies genetic material so that other techniques can identify aspects of the genes or match them to known genes.

primer   (in genetics) A sequence of nucleotides that is the complement for a short part of a strand of DNA that someone wants to find. In the polymerase chain reaction, or PCR, the primer finds the end of a targeted DNA length and starts the process of copying it over and over.

species    A group of similar organisms capable of producing offspring that can survive and reproduce.

variant     A version of something that may come in different forms. (in genetics) A gene having a slight mutation that may have left its host species somewhat better adapted for its environment.