title: Quantification of the carbazole 1,9a-dioxygenase gene by real-time competitive PCR combined with co-extraction of internal standards.
abstract: The fluorogenic probe assay, competitive polymerase chain reaction (PCR) and co-extraction with internal standard cells were combined to develop a rapid, sensitive, and accurate quantification method for the copy number of a target carbazole 1,9a-dioxygenase gene (carAa) and the cell number of Pseudomonas sp. strain CA10. The internal standard DNA was modified by replacement of a 20-bp long region with one for binding a specific probe in fluorogenic PCR (TaqMan). The resultant DNA fragment was similar to the corresponding region of the intact carAa gene in terms of G+C content. When used as a competitor in the PCR reaction, the internal standard DNA was distinguishable from the target carAa gene by two specific fluorogenic probes with different fluorescence labels, and was automatically detected in a single tube using the ABI7700 sequence detection system. To minimize variations in the efficiency of cell lysis and DNA extraction between the samples, the co-extraction method was combined. A mini-transposon was used to introduce competitor DNA into the genome of other pseudomonads, and the resultant construct was used as the standard cell. After the addition of a fixed amount of the internal standard cells to soil samples, total DNA was extracted (co-extraction). Using this method, the copy number of the carAa gene and the cell number of strain CA10 in soil samples could be quantified rapidly.
authors.affiliation: Biotechnology Research Center, The University of Tokyo, Japan.
authors.forename: J
authors.initials: J
authors.lastname: Widada
authors.forename: H
authors.initials: H
authors.lastname: Nojiri
authors.forename: K
authors.initials: K
authors.lastname: Kasuga
authors.forename: T
authors.initials: T
authors.lastname: Yoshida
authors.forename: H
authors.initials: H
authors.lastname: Habe
authors.forename: T
authors.initials: T
authors.lastname: Omori
mesh_terms: D001426:Bacterial Proteins; D001667:Binding, Competitive; D017931:DNA Primers / Q000235:genetics; D015342:DNA Probes / Q000235:genetics; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics / Q000302:isolation & purification; D049308:Dioxygenases; D004587:Electrophoresis, Agar Gel; D005456:Fluorescent Dyes; D010105:Oxygenases / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods* / Q000592:standards*; D011549:Pseudomonas / Q000201:enzymology / Q000235:genetics* / Q000302:isolation & purification*; D012015:Reference Standards; D012680:Sensitivity and Specificity; D012988:Soil Microbiology
chemical_list: D001426:Bacterial Proteins; D017931:DNA Primers; D015342:DNA Probes; D004269:DNA, Bacterial; D005456:Fluorescent Dyes; D010105:Oxygenases; D049308:Dioxygenases; C108434:carbazole 1,9a-dioxygenase