denaturation-annealing-extension cycling

How does PCR turn one copy into a billion? Not in one giant step, but by repeating a short, three-temperature dance over and over. Each pass through the dance roughly doubles the target, and a machine called a thermal cycler simply changes the tube's temperature on a timer to drive it. The dance is denaturation, then annealing, then extension.

Denaturation: heat to about 95 degrees Celsius. The hydrogen bonds holding the double helix break and the two strands separate, giving single-stranded templates. Annealing: cool to roughly 50 to 65 degrees Celsius. At this lower temperature the short primers find and base-pair with their matching sequences on the templates. Extension: warm to about 72 degrees Celsius, the temperature Taq polymerase likes best. Taq starts at each primer's 3' end and builds a new complementary strand, copying the template. Then the cycle repeats. Crucially, the new strands made in one cycle become templates in the next, so the number of target molecules grows geometrically: 1, 2, 4, 8, 16, and so on — exponential growth.

This temperature loop is the engine of PCR, and tuning it matters. If the annealing temperature is too low, primers stick loosely to near-matches and you get nonspecific products; too high and they will not bind at all. In practice the exponential growth does not continue forever — as reagents run low and product accumulates, the reaction reaches a plateau, which is why simply counting final product is a poor way to measure starting amount (that is what quantitative PCR was invented to fix).