Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples

Appl Environ Microbiol. 2011 Jun;77(11):3551-7. doi: 10.1128/AEM.00331-11. Epub 2011 Apr 15.

Abstract

Aromatic dioxygenase genes have long been of interest for bioremediation and aromatic carbon cycling studies. To date, 115 primers and probes have been designed and used to analyze dioxygenase gene diversities in environmental samples. Here we analyze those primers' specificities, coverages, and PCR product lengths compared to known aromatic dioxygenase genes based on in silico analysis as well as summarize their differing advantages or effectiveness from over 50 reported experimental studies. We also provide some guidance for primer use in future studies.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Computational Biology
  • DNA Primers / genetics*
  • Dioxygenases / genetics*
  • Dioxygenases / metabolism
  • Environmental Microbiology*
  • Genetic Variation
  • Hydrocarbons, Aromatic / metabolism
  • Metagenomics*
  • Polymerase Chain Reaction / methods*

Substances

  • DNA Primers
  • Hydrocarbons, Aromatic
  • Dioxygenases