PCR VIRTUAL LAB
PCR (short for Polymerase Chain Reaction) is a relatively simple and inexpensive tool that you can use to focus in on a segment of DNA and copy it billions of times over. PCR is used every day to diagnose diseases, identify bacteria and viruses, match criminals to crime scenes, and in many other ways. Step up to the virtual lab bench and see how it works!
What are these things doing in my PCR reaction?
Primers are short pieces of DNA that are made in a laboratory. Since they're custom built, primers can have any sequence of nucleotides you'd like.
In a PCR experiment, two primers are designed to match to the segment of DNA you want to copy. Through complementary base pairing, one primer attaches to the top strand at one end of your segment of interest, and the other primer attaches to the bottom strand at the other end. In most cases, 2 primers that are 20 or so nucleotides long will target just one place in the entire genome.
Primers are also necessary because DNA polymerase can't attach at just any old place and start copying away. It can only add onto an existing piece of DNA.
DNA Polymerase is a naturally-occurring complex of proteins whose function is to copy a cell's DNA before it divides in two. When a DNA polymerase molecule bumps into a primer that's base-paired with a longer piece of DNA, it attaches itself near the end of the primer and starts adding nucleotides. (In nature, these primers are made by an enzyme called primase).
The DNA polymerase in our bodies breaks down at temperatures well below 95 °C (203 °F) -- the temperature necessary to separate two complementary strands of DNA in a test tube. The DNA polymerase that's most often used in PCR comes from a strain of bacteria called Thermus aquaticus that live in the hot springs of Yellowstone National Park. It can survive near boiling temperatures and works quite well at 72 °C (162 °F).
Nucleotides are the building blocks that DNA molecules are made of. You add a mixture of four types of nucleotides to your PCR reaction -- A's, C's, G's and T's. DNA polymerase grabs nucleotides that are floating in the liquid around it and attaches them to the end of a primer.