PCR — the three temperatures and why they are what they are
Each cycle has three steps, and each temperature is doing something specific. Denaturation near 95 degrees separates the strands by breaking hydrogen bonds without touching the phosphodiester backbone. Annealing between roughly 50 and 65 degrees lets primers bind, and this is the step you tune: too low and primers bind non-specifically, too high and they do not bind at all, so annealing temperature is set from the primers' melting temperature. Extension at 72 degrees is the optimum for Taq polymerase, isolated from a hot-spring bacterium precisely because it survives the denaturation step that would destroy a human polymerase. Amplification is exponential — n cycles give roughly two to the n copies — which is why contamination is so consequential.