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Sensors 2018, 18(8), 2646; https://doi.org/10.3390/s18082646

The Implications of Fragmented Genomic DNA Size Range on the Hybridization Efficiency in NanoGene Assay

1
Department of Civil Engineering, Auburn University, Auburn, AL 36849, USA
2
School of Electrical Engineering, Korea University, Seoul 02841, Korea
3
Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03760, Korea
*
Author to whom correspondence should be addressed.
Received: 18 July 2018 / Revised: 10 August 2018 / Accepted: 10 August 2018 / Published: 13 August 2018
(This article belongs to the Section Biosensors)
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Abstract

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. View Full-Text
Keywords: DNA fragmentation; optimum size; quantification capability; hybridization efficiency; magnetic beads; quantum dots DNA fragmentation; optimum size; quantification capability; hybridization efficiency; magnetic beads; quantum dots
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
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Wang, X.; Chua, B.; Son, A. The Implications of Fragmented Genomic DNA Size Range on the Hybridization Efficiency in NanoGene Assay. Sensors 2018, 18, 2646.

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