Development of a DNA biosensor based on magnetic nanoparticles for the detection of Ganoderma boninense

The unique electrochemical and optical properties of nanoparticles combined with the relative ease with which their shape and size can be controlled is currently showing promise in the development of new biosensors. In particular, magnetic nanoparticles are of great interest in DNA sensors for their...

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Main Author:	Hushiarian, Roozbeh
Format:	Thesis
Language:	English
Published:	2015
Subjects:	Nanoparticles - Magnetic properties Nanostructures - Magnetic properties Ganoderma
Online Access:	http://psasir.upm.edu.my/id/eprint/65438/1/FS%202015%2042IR.pdf
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id	my-upm-ir.65438
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spelling	my-upm-ir.654382018-09-14T08:20:05Z Development of a DNA biosensor based on magnetic nanoparticles for the detection of Ganoderma boninense 2015-01 Hushiarian, Roozbeh The unique electrochemical and optical properties of nanoparticles combined with the relative ease with which their shape and size can be controlled is currently showing promise in the development of new biosensors. In particular, magnetic nanoparticles are of great interest in DNA sensors for their ability to both separate biological macromolecules as well as to optimize DNA hybridization. The intent of this research was to address the gap in knowledge about the fundamentals of the molecular interactions between DNA and nanoparticles, especially magnetic nanoparticles. The pathogen selected was the basidiomycete Ganoderma boninense, the main cause of basal stem rot disease which continues its devastating effect on oil palm trees in South East Asia. A designed DNA sequence and its complementary strains – a sequence of 18s rRNA gene of Ganoderma boninense - was taken as the template. The work in this thesis was built on understood mechanisms from previous studies with the goal of further optimizing a DNA biosensor. One major part of the research involved the design and construction of an optical magnetic nanoparticle–based biosensor using quantum dots as markers. This clearly demonstrated that DNA can bind to the surface of iron oxide nanoparticles and that they can act as effective biomolecule carriers. The detection limit of the designed optical nanosensor was calculated as 2.19×10-9 M. The sensitivity of the system was increased by 20% using a two step hybridization method. A new innovative software package was used to better understand the mechanism of detection. The other major section introduced an electrochemical method for sensing and conclusively showed that it could bring a representative sequence of an analyte to the biorecognition surface. The electrochemical sensor based on magnetic nanoparticles showed a sensitivity of 1.1×10-16 M and then this method was further extended to successfully increase the selectivity of this system by the novel use of DNA ligase. The indirect detection of the target DNA using DNA ligase was successfully performed with a detection limit of 5.37×10-14 M. This creative ligation-based mechanism was ultimately employed to detect the extracted genomic DNA of the pathogen. The methods and results in this study enhance the understanding of molecular interactions between DNA and nanoparticles and contribute to the body of work attempting to address the outstanding issue of improving the selectivity and sensitivity of DNA biosensors. Nanoparticles - Magnetic properties Nanostructures - Magnetic properties Ganoderma 2015-01 Thesis http://psasir.upm.edu.my/id/eprint/65438/ http://psasir.upm.edu.my/id/eprint/65438/1/FS%202015%2042IR.pdf text en public doctoral Universiti Putra Malaysia Nanoparticles - Magnetic properties Nanostructures - Magnetic properties Ganoderma
institution	Universiti Putra Malaysia
collection	PSAS Institutional Repository
language	English
topic	Nanoparticles - Magnetic properties Nanostructures - Magnetic properties Ganoderma
spellingShingle	Nanoparticles - Magnetic properties Nanostructures - Magnetic properties Ganoderma Hushiarian, Roozbeh Development of a DNA biosensor based on magnetic nanoparticles for the detection of Ganoderma boninense
description	The unique electrochemical and optical properties of nanoparticles combined with the relative ease with which their shape and size can be controlled is currently showing promise in the development of new biosensors. In particular, magnetic nanoparticles are of great interest in DNA sensors for their ability to both separate biological macromolecules as well as to optimize DNA hybridization. The intent of this research was to address the gap in knowledge about the fundamentals of the molecular interactions between DNA and nanoparticles, especially magnetic nanoparticles. The pathogen selected was the basidiomycete Ganoderma boninense, the main cause of basal stem rot disease which continues its devastating effect on oil palm trees in South East Asia. A designed DNA sequence and its complementary strains – a sequence of 18s rRNA gene of Ganoderma boninense - was taken as the template. The work in this thesis was built on understood mechanisms from previous studies with the goal of further optimizing a DNA biosensor. One major part of the research involved the design and construction of an optical magnetic nanoparticle–based biosensor using quantum dots as markers. This clearly demonstrated that DNA can bind to the surface of iron oxide nanoparticles and that they can act as effective biomolecule carriers. The detection limit of the designed optical nanosensor was calculated as 2.19×10-9 M. The sensitivity of the system was increased by 20% using a two step hybridization method. A new innovative software package was used to better understand the mechanism of detection. The other major section introduced an electrochemical method for sensing and conclusively showed that it could bring a representative sequence of an analyte to the biorecognition surface. The electrochemical sensor based on magnetic nanoparticles showed a sensitivity of 1.1×10-16 M and then this method was further extended to successfully increase the selectivity of this system by the novel use of DNA ligase. The indirect detection of the target DNA using DNA ligase was successfully performed with a detection limit of 5.37×10-14 M. This creative ligation-based mechanism was ultimately employed to detect the extracted genomic DNA of the pathogen. The methods and results in this study enhance the understanding of molecular interactions between DNA and nanoparticles and contribute to the body of work attempting to address the outstanding issue of improving the selectivity and sensitivity of DNA biosensors.
format	Thesis
qualification_level	Doctorate
author	Hushiarian, Roozbeh
author_facet	Hushiarian, Roozbeh
author_sort	Hushiarian, Roozbeh
title	Development of a DNA biosensor based on magnetic nanoparticles for the detection of Ganoderma boninense
title_short	Development of a DNA biosensor based on magnetic nanoparticles for the detection of Ganoderma boninense
title_full	Development of a DNA biosensor based on magnetic nanoparticles for the detection of Ganoderma boninense
title_fullStr	Development of a DNA biosensor based on magnetic nanoparticles for the detection of Ganoderma boninense
title_full_unstemmed	Development of a DNA biosensor based on magnetic nanoparticles for the detection of Ganoderma boninense
title_sort	development of a dna biosensor based on magnetic nanoparticles for the detection of ganoderma boninense
granting_institution	Universiti Putra Malaysia
publishDate	2015
url	http://psasir.upm.edu.my/id/eprint/65438/1/FS%202015%2042IR.pdf
_version_	1747812337560059904

Development of a DNA biosensor based on magnetic nanoparticles for the detection of Ganoderma boninense

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