Touchdown polymerase chain reaction

At temperatures just above this point, only very specific base pairing between the primer and the template will occur.

Nonspecific primer binding obscures polymerase chain reaction results, as the nonspecific sequences to which primers anneal in early steps of amplification will "swamp out" any specific sequences because of the exponential nature of polymerase amplification.

[2] The earliest steps of a touchdown polymerase chain reaction cycle have high annealing temperatures.

The primer will anneal at the highest temperature which is least-permissive of nonspecific binding that it is able to tolerate.

If the primer initially (during the higher-temperature phases) binds to the sequence of interest, subsequent rounds of polymerase chain reaction can be performed upon the product to further amplify those fragments.

Scheme of touchdown PCR. The first annealing between primer and DNA occurs at the initial temperature, the second after the temperature has been lowered by . Therefore, the product of the second annealing is disadvantaged by .