Quantitative DNA hybridization in solution using magnetic/luminescent core-shell nanoparticles

Ahjeong Son; Dosi Dosev; Mikaela Nichkova; Zhiya Ma; Ian M. Kennedy; Kate M. Scow; Krassimira R. Hristova

doi:10.1016/j.ab.2007.08.001

Quantitative DNA hybridization in solution using magnetic/luminescent core-shell nanoparticles

Ahjeong Son, Dosi Dosev, Mikaela Nichkova, Zhiya Ma, Ian M. Kennedy, Kate M. Scow, Krassimira R. Hristova

Department of Environmental Science & Engineering

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

55 Scopus citations

Abstract

Nanoscale magnetic/luminescent core-shell particles were used for DNA quantification in a hybridization-in-solution approach. We demonstrated a rapid, simple, and non-polymerase chain reaction-based DNA hybridization-in-solution assay for quantifying bacteria capable of biodegrading methyl tertiary-butyl ether. Fe₃O₄/Eu:Gd₂O₃ core-shell nanoparticles synthesized by spray pyrolysis were biofunctionalized with NeutrAvidin. Following immobilization of a biotinylated probe DNA on the particles' surfaces via passive adsorption, target DNA labeled with fluorescein isothiocyanate was hybridized with probe DNA. The hybridized DNA complex was separated from solution with a magnet, while nonhybridized DNA remained in solution. The normalized fluorescence (fluorescein isothiocyanate/nanoparticles) measured with a spectrofluorometer indicated a linear quantification (R² = 0.98) of the target bacterial 16 S rDNA. The rate of hybridization increased concurrently with the target DNA concentration. In addition, this approach differentiated between the signal outputs from perfectly complementary target and two-base mismatched target DNA in a range of concentrations, showing the specificity of the assay and the possibility for environmental applications.

Original language	English
Pages (from-to)	186-194
Number of pages	9
Journal	Analytical Biochemistry
Volume	370
Issue number	2
DOIs	https://doi.org/10.1016/j.ab.2007.08.001
State	Published - 15 Nov 2007

Bibliographical note

Funding Information:
This article was made possible by Grant 5 P42 ES04699-16 from the National Institute of Environmental Health Sciences (NIEHS). The support of the National Science Foundation through Grant DBI-02662 as part of the Nanoscale Science and Engineering Program is also appreciated. The project was also supported by the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service, Grant 2005-35603-16280.

Keywords

DNA
Hybridization-in-solution
Lanthanide oxide
Magnetic particles
Methyl tertiary-butyl ether
Nanoparticles

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10.1016/j.ab.2007.08.001

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title = "Quantitative DNA hybridization in solution using magnetic/luminescent core-shell nanoparticles",

abstract = "Nanoscale magnetic/luminescent core-shell particles were used for DNA quantification in a hybridization-in-solution approach. We demonstrated a rapid, simple, and non-polymerase chain reaction-based DNA hybridization-in-solution assay for quantifying bacteria capable of biodegrading methyl tertiary-butyl ether. Fe3O4/Eu:Gd2O3 core-shell nanoparticles synthesized by spray pyrolysis were biofunctionalized with NeutrAvidin. Following immobilization of a biotinylated probe DNA on the particles' surfaces via passive adsorption, target DNA labeled with fluorescein isothiocyanate was hybridized with probe DNA. The hybridized DNA complex was separated from solution with a magnet, while nonhybridized DNA remained in solution. The normalized fluorescence (fluorescein isothiocyanate/nanoparticles) measured with a spectrofluorometer indicated a linear quantification (R2 = 0.98) of the target bacterial 16 S rDNA. The rate of hybridization increased concurrently with the target DNA concentration. In addition, this approach differentiated between the signal outputs from perfectly complementary target and two-base mismatched target DNA in a range of concentrations, showing the specificity of the assay and the possibility for environmental applications.",

keywords = "DNA, Hybridization-in-solution, Lanthanide oxide, Magnetic particles, Methyl tertiary-butyl ether, Nanoparticles",

author = "Ahjeong Son and Dosi Dosev and Mikaela Nichkova and Zhiya Ma and Kennedy, {Ian M.} and Scow, {Kate M.} and Hristova, {Krassimira R.}",

note = "Funding Information: This article was made possible by Grant 5 P42 ES04699-16 from the National Institute of Environmental Health Sciences (NIEHS). The support of the National Science Foundation through Grant DBI-02662 as part of the Nanoscale Science and Engineering Program is also appreciated. The project was also supported by the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service, Grant 2005-35603-16280.",

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doi = "10.1016/j.ab.2007.08.001",

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journal = "Analytical Biochemistry",

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AU - Son, Ahjeong

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AU - Ma, Zhiya

AU - Kennedy, Ian M.

AU - Scow, Kate M.

AU - Hristova, Krassimira R.

N1 - Funding Information: This article was made possible by Grant 5 P42 ES04699-16 from the National Institute of Environmental Health Sciences (NIEHS). The support of the National Science Foundation through Grant DBI-02662 as part of the Nanoscale Science and Engineering Program is also appreciated. The project was also supported by the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service, Grant 2005-35603-16280.

PY - 2007/11/15

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N2 - Nanoscale magnetic/luminescent core-shell particles were used for DNA quantification in a hybridization-in-solution approach. We demonstrated a rapid, simple, and non-polymerase chain reaction-based DNA hybridization-in-solution assay for quantifying bacteria capable of biodegrading methyl tertiary-butyl ether. Fe3O4/Eu:Gd2O3 core-shell nanoparticles synthesized by spray pyrolysis were biofunctionalized with NeutrAvidin. Following immobilization of a biotinylated probe DNA on the particles' surfaces via passive adsorption, target DNA labeled with fluorescein isothiocyanate was hybridized with probe DNA. The hybridized DNA complex was separated from solution with a magnet, while nonhybridized DNA remained in solution. The normalized fluorescence (fluorescein isothiocyanate/nanoparticles) measured with a spectrofluorometer indicated a linear quantification (R2 = 0.98) of the target bacterial 16 S rDNA. The rate of hybridization increased concurrently with the target DNA concentration. In addition, this approach differentiated between the signal outputs from perfectly complementary target and two-base mismatched target DNA in a range of concentrations, showing the specificity of the assay and the possibility for environmental applications.

AB - Nanoscale magnetic/luminescent core-shell particles were used for DNA quantification in a hybridization-in-solution approach. We demonstrated a rapid, simple, and non-polymerase chain reaction-based DNA hybridization-in-solution assay for quantifying bacteria capable of biodegrading methyl tertiary-butyl ether. Fe3O4/Eu:Gd2O3 core-shell nanoparticles synthesized by spray pyrolysis were biofunctionalized with NeutrAvidin. Following immobilization of a biotinylated probe DNA on the particles' surfaces via passive adsorption, target DNA labeled with fluorescein isothiocyanate was hybridized with probe DNA. The hybridized DNA complex was separated from solution with a magnet, while nonhybridized DNA remained in solution. The normalized fluorescence (fluorescein isothiocyanate/nanoparticles) measured with a spectrofluorometer indicated a linear quantification (R2 = 0.98) of the target bacterial 16 S rDNA. The rate of hybridization increased concurrently with the target DNA concentration. In addition, this approach differentiated between the signal outputs from perfectly complementary target and two-base mismatched target DNA in a range of concentrations, showing the specificity of the assay and the possibility for environmental applications.

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KW - Hybridization-in-solution

KW - Lanthanide oxide

KW - Magnetic particles

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KW - Nanoparticles

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Quantitative DNA hybridization in solution using magnetic/luminescent core-shell nanoparticles

Abstract

Bibliographical note

Keywords

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