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
reactionA'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.