Specificity of randomly generated genomic DNA fragment probes on a DNA array |
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Authors: | Tobino Tomohiro Kurisu Futoshi Kasuga Ikuro Furumai Hiroaki |
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Affiliation: | Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan. t_tobino@esc.u-tokyo.ac.jp |
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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. |
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