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For PCR, the melting temp plays an important role foravoiding unspecific binding to DNA sequences. It controls/allows binding to specific target sequences of the DNA in the "annealing" step of PCR. Primer Annealing Temperature: The primer melting temperature is the estimate of the DNA-DNA hybrid stability and critical in determining the annealing temperature. Too high Ta will produce insufficient primer-template hybridization resulting in low PCR product yield.