PCR co-amplification can lead to DNA recombination, which can be reduced by increasing Taq polymerase elongation time, highlighting a potential artifact in studying heterogeneous genetic material or a method to create chimeric molecules.
PCR co-amplification of two distinct HIV1 tat gene sequences lead to the formation of recombinant DNA molecules. The frequency of such recombinants, up to 5.4% of all amplified molecules, could be decreased 2.7 fold by a 6 fold increase in Taq DNA polymerase elongation time. Crossover sites mapped essentially to three discrete regions suggesting specific Taq DNA polymerase pause or termination sites. PCR mediated recombination may be a problem when studying heterogeneous genetic material such as RNA viruses, multigene families, or repetitive sequences. This phenomenon can be exploited to create chimeric molecules from related sequences.
Meyerhans et al. (Mon,) studied this question.
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