DNA recombination during PCR

Nucleic Acids Res. 1990 Apr 11;18(7):1687-91. doi: 10.1093/nar/18.7.1687.


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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Chimera
  • Cloning, Molecular / methods
  • DNA, Recombinant / metabolism*
  • Gene Amplification*
  • Gene Products, tat / genetics
  • Genes, Viral*
  • Genes, tat*
  • HIV-1 / genetics*
  • Molecular Sequence Data
  • Oligonucleotide Probes
  • Plasmids
  • Polymerase Chain Reaction*
  • Recombination, Genetic*
  • Sequence Homology, Nucleic Acid
  • tat Gene Products, Human Immunodeficiency Virus


  • DNA, Recombinant
  • Gene Products, tat
  • Oligonucleotide Probes
  • tat Gene Products, Human Immunodeficiency Virus