The implications of fragmented genomic DNA size range on the hybridization efficiency in NanoGene assay

Xiaofang Wang; Beelee Chua; Ahjeong Son

doi:10.3390/s18082646

The implications of fragmented genomic DNA size range on the hybridization efficiency in NanoGene assay

Xiaofang Wang, Beelee Chua, Ahjeong Son

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

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.

Original language	English
Article number	2646
Journal	Sensors (Switzerland)
Volume	18
Issue number	8
DOIs	https://doi.org/10.3390/s18082646
Publication status	Published - 2018 Aug 13

Bibliographical note

Funding Information:
Funding: This work was supported by National Research Foundation of Korea (NRF-2015R1D1A1A-01060317 and NRF-2017R1A2B-4005133).

Publisher Copyright:
© 2018 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

DNA fragmentation
Hybridization efficiency
Magnetic beads
Optimum size
Quantification capability
Quantum dots

ASJC Scopus subject areas

Analytical Chemistry
Biochemistry
Atomic and Molecular Physics, and Optics
Instrumentation
Electrical and Electronic Engineering

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10.3390/s18082646

Cite this

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title = "The implications of fragmented genomic DNA size range on the hybridization efficiency in NanoGene assay",

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.",

keywords = "DNA fragmentation, Hybridization efficiency, Magnetic beads, Optimum size, Quantification capability, Quantum dots",

author = "Xiaofang Wang and Beelee Chua and Ahjeong Son",

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AU - Chua, Beelee

AU - Son, Ahjeong

N1 - Funding Information: Funding: This work was supported by National Research Foundation of Korea (NRF-2015R1D1A1A-01060317 and NRF-2017R1A2B-4005133). Publisher Copyright: © 2018 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2018/8/13

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N2 - 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.

AB - 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.

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KW - Hybridization efficiency

KW - Magnetic beads

KW - Optimum size

KW - Quantification capability

KW - Quantum dots

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The implications of fragmented genomic DNA size range on the hybridization efficiency in NanoGene assay

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

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