Step 1: Denaturation: This step uses high heat (around 95°C) to denature the double helix DNA structure into single strands.
Step 2: Annealing step uses a lower heat to allow the primers in the reaction mix to bind to the template which is now single stranded. Annealing temperatures are usually around 60°C but can vary depending on the design of the primers.
Step 3 is the extension step, where the temperature is again increased to about 72°C to allow for optimal performance of the taq polymerase enzyme which attaches to the site where the primer binds to the template. During this step, the taq moves along the strand incorporating free nucleotides into the sequence to generate a double stranded DNA.
Step 4: End of cycle. This is the duration set out by the thermocycler for the extension step. The next cycle starts again from step 1 through step 3 to complete a second cyle. 35 to 40 cycles can be completed for good results.