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 journalArticle

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 languageEnglish
Article number2646
JournalSensors (Switzerland)
Volume18
Issue number8
DOIs
Publication statusPublished - 2018 Aug 13

Fingerprint

Assays
DNA
deoxyribonucleic acid
Nucleic Acid Hybridization
Bacterial DNA
Sonication
DNA Probes
DNA Fragmentation
Fluorescence In Situ Hybridization
Microarrays
bacteria
Bacteria
Fluorescence
fragmentation
fluorescence
probes

Keywords

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

ASJC Scopus subject areas

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

Cite this

The implications of fragmented genomic DNA size range on the hybridization efficiency in NanoGene assay. / Wang, Xiaofang; Chua, Beelee; Son, Ahjeong.

In: Sensors (Switzerland), Vol. 18, No. 8, 2646, 13.08.2018.

Research output: Contribution to journalArticle

@article{102f70af95e74fa39952181cd56e878b,
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",
year = "2018",
month = "8",
day = "13",
doi = "10.3390/s18082646",
language = "English",
volume = "18",
journal = "Sensors (Switzerland)",
issn = "1424-8220",
publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",
number = "8",

}

TY - JOUR

T1 - The implications of fragmented genomic DNA size range on the hybridization efficiency in NanoGene assay

AU - Wang, Xiaofang

AU - Chua, Beelee

AU - Son, Ahjeong

PY - 2018/8/13

Y1 - 2018/8/13

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.

KW - DNA fragmentation

KW - Hybridization efficiency

KW - Magnetic beads

KW - Optimum size

KW - Quantification capability

KW - Quantum dots

UR - http://www.scopus.com/inward/record.url?scp=85052121445&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85052121445&partnerID=8YFLogxK

U2 - 10.3390/s18082646

DO - 10.3390/s18082646

M3 - Article

VL - 18

JO - Sensors (Switzerland)

JF - Sensors (Switzerland)

SN - 1424-8220

IS - 8

M1 - 2646

ER -