The term plateau effect is used to describe the attenuation of the normally exponential rate of product accumulation in PCR. The attenuation occurs during the late PCR cycles when the accumulation of product reaches 0.3 to 1 picomole. Depending on reaction conditions and thermal cycling, one or more of the following may influence when the plateau is reached:

• Depletion of substrates (dNTPs or primers)
• Stability of the reactants (dNTPs or enzyme) particularly at the denaturation temperature
• End-product inhibition (pyrophosphate, duplex DNA)
• Competition for reactants by nonspecific products or primer-dimer
• Reannealing of specific product at concentration above 10^-8 M (may decrease the extension rate or processivity of Taq DNA polymerase or change branch-migration of product strands and displacement of primers)
• Incomplete denaturation/strand separation of product at high product concentration¹¹

An important consequence of reaching plateau is that nonspecific products resulting from mispriming events, initially present at low concentration, may continue to amplify preferentially. Optimizing the number of PCR cycles is the best way to avoid amplifying background products.

Summary

PCR yield is directly affected by the primer design. There are commercially available primer design software packages that are commonly used to assist scientists in designing primers.

Read about primer design software packages at the Chemical Science and Technology home page of NIST.

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