Department of Civil Engineering, Auburn University, Auburn, AL 36849, USA.
School of Electrical Engineering, Korea University, Seoul 02841, Korea.
Sensors (Basel). 2018 Aug 13;18(8):2646. doi: 10.3390/s18082646.
DNA hybridization-based assays are well known for their ability to detect and quantify specific bacteria. Assays that employ DNA hybridization include a NanoGene assay, fluorescence in situ hybridization, and microarrays. Involved in DNA hybridization, fragmentation of genomic DNA (gDNA) is necessary to increase the accessibility of the probe DNA to the target gDNA. However, there has been no thorough and systematic characterization of different fragmented gDNA sizes and their effects on hybridization efficiency. An optimum fragmented size range of gDNA for the NanoGene assay is hypothesized in this study. Bacterial gDNA is fragmented via sonication into different size ranges prior to the NanoGene assay. The optimum size range of gDNA is determined via the comparison of respective hybridization efficiencies (in the form of quantification capabilities). Different incubation durations are also investigated. Finally, the quantification capability of the fragmented (at optimum size range) and unfragmented gDNA is compared.
基于 DNA 杂交的检测方法以其检测和定量特定细菌的能力而闻名。采用 DNA 杂交的检测方法包括 NanoGene 检测、荧光原位杂交和微阵列。在 DNA 杂交中，基因组 DNA（gDNA）的片段化对于增加探针 DNA 与靶 gDNA 的可及性是必要的。然而，不同的 gDNA 片段大小及其对杂交效率的影响尚未得到全面和系统的描述。本研究假设 NanoGene 检测中 gDNA 的最佳片段化大小范围。在进行 NanoGene 检测之前，通过超声处理将细菌 gDNA 片段化为不同的大小范围。通过比较各自的杂交效率（以定量能力的形式）来确定 gDNA 的最佳大小范围。还研究了不同的孵育时间。最后，比较了（在最佳大小范围内）片段化和未片段化 gDNA 的定量能力。
