DNA recombination during PCR

Abstract

PCR co-amplification of two distinct HIV1 far 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 chlmerlc molecules from related sequences