Calculating the optimal PCR annealing temperature

MacVector has several tools to help with primer design and testing. The Analyze | Primer Design/Test (Pairs) function uses the popular Primer3 algorithm to find suitable pairs of primers to amplify specified segments of DNA. You can also enter pairs of pre-designed primers and test their suitability for use in PCR. In both cases, the Tm of each primer is reported, along with the optimal annealing temperature (Ta).


The optimal annealing temperature (degrees C) is calculated as follows (from W. Rychlik, W.J. Spencer, and R. E. Rhoads, Nucl.Acids.Res. 18:6409–6412(1990));

(Lowest Primer Tm x 0.3) + (Product Tm x 0.7) - 14.9

This means that you can get an optimal annealing temperature for a PCR experiment that is significantly different from the optimal annealing temperature for an individual primer (e.g. in a sequencing experiment) because of the large influence of the product in the calculation.

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