title: Specificity of randomly generated genomic DNA fragment probes on a DNA array.
abstract: The use of randomly generated DNA fragment sequences as probes on DNA arrays offers a unique potential for exploring unsequenced microorganisms. In this study, the detection specificity was evaluated with respect to probe-target sequence similarity using genomic DNAs of four Pseudomonas strains. Genome fragments averaging 2000 bp were found to be specific enough to discriminate 85-90% similarity under highly stringent hybridization conditions. Such stringent conditions compromised signal intensities; however, specific signals remained detectable at the highest stringency (at 75 °C hybridization) with negligible false negatives. These results suggest that, without any probe design or selection, genomic fragments can provide a reasonable specificity for microbial diagnostics or species delineation by DNA-DNA similarities.
authors.affiliation: Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan. t_tobino@esc.u-tokyo.ac.jp
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Tobino
authors.forename: Futoshi
authors.initials: F
authors.lastname: Kurisu
authors.forename: Ikuro
authors.initials: I
authors.lastname: Kasuga
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Furumai
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics; D046228:Microarray Analysis / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D015345:Oligonucleotide Probes / Q000235:genetics; D011549:Pseudomonas / Q000235:genetics*; D012680:Sensitivity and Specificity
chemical_list: D004269:DNA, Bacterial; D015345:Oligonucleotide Probes