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.
Bibliographical noteFunding Information:
Funding: This work was supported by National Research Foundation of Korea (NRF-2015R1D1A1A-01060317 and NRF-2017R1A2B-4005133).
© 2018 by the authors. Licensee MDPI, Basel, Switzerland.
- DNA fragmentation
- Hybridization efficiency
- Magnetic beads
- Optimum size
- Quantification capability
- Quantum dots