Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
FEMS Microbiol Lett. 2012 Mar;328(1):86-9. doi: 10.1111/j.1574-6968.2011.02486.x. Epub 2012 Jan 4.
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.
随机生成的 DNA 片段序列用作 DNA 芯片上的探针，为探索未测序的微生物提供了独特的潜力。在这项研究中，使用了四种假单胞菌属菌株的基因组 DNA 来评估探针-靶序列相似性的检测特异性。发现平均长度为 2000bp 的基因组片段在高度严格的杂交条件下具有足够的特异性，可以区分 85-90%的相似性。然而，这种严格的条件会降低信号强度；但是，在最高严格条件下（在 75°C 杂交）仍然可以检测到特异性信号，并且假阴性率可以忽略不计。这些结果表明，无需任何探针设计或选择，基因组片段就可以为微生物诊断或通过 DNA-DNA 相似性进行物种划分提供合理的特异性。
