title: Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples.
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.
authors.affiliation: Center for Microbial Ecology, Michigan State University, 540 Plant and Soil Sciences Building, East Lansing, MI 48824, USA.
authors.forename: Shoko
authors.initials: S
authors.lastname: Iwai
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Johnson
authors.forename: Benli
authors.initials: B
authors.lastname: Chai
authors.forename: Syed A
authors.initials: SA
authors.lastname: Hashsham
authors.forename: James M
authors.initials: JM
authors.lastname: Tiedje
mesh_terms: D019295:Computational Biology; D017931:DNA Primers / Q000235:genetics*; D049308:Dioxygenases / Q000235:genetics* / Q000378:metabolism; D004783:Environmental Microbiology; D014644:Genetic Variation; D006841:Hydrocarbons, Aromatic / Q000378:metabolism; D056186:Metagenomics; D016133:Polymerase Chain Reaction / Q000379:methods*
chemical_list: D017931:DNA Primers; D006841:Hydrocarbons, Aromatic; D049308:Dioxygenases