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Chemically tagged DNA probes for sensing of DNA biomarkers using Lab-on-a-chip technology

Chemically tagged DNA probes for sensing of DNA biomarkers using Lab-on-a-chip technology
Chemically tagged DNA probes for sensing of DNA biomarkers using Lab-on-a-chip technology
DNA methylation is a common epigenetic abnormality found in cancer. Although a high content of DNA methylation is found in cancer patients, the amount is still very low and multiple round of amplification is necessary. In addition, multiple genes are methylated in cancer patients. Therefore a high sensitivity and multiplexed sensor is desired for methylated DNA detection. This work develops a single sensor device and a multi sensor device multiplex work. To show the capability of these devices, bladder cancer biomarkers are selected for demonstration. In bladder cancer, three genes (DAPK, E. Cadherin and RARβ) are found to be methylated in the promoter region. A hairpin probe was designed with a redox active chemical tag incorporated into the design. Anthraquinone and porphyrin modified DNA probes were synthesised and compared with the commercially available methylene blue. Simultaneous detection of these three genes is essential for bladder cancer diagnosis. This work shows that with the multi sensor device, all three biomarkers can be detected in single run using only 20 minutes operational time, with a limit of detection of 250 fM.

Alongside detection of DNA methylation, an additional biomarker found in bladder cancer patients, microRNA, was investigated. Hairpin and linear probe designs were compared. The miRNA was detected in spiked Surine (urine negative control) to demonstrate the feasibility of the system with detection in human samples.
University of Southampton
Pursey, Joanna Patricia
f5e36098-76a3-4e39-9d32-7827879799aa
Pursey, Joanna Patricia
f5e36098-76a3-4e39-9d32-7827879799aa
Stulz, Eugen
9a6c04cf-32ca-442b-9281-bbf3d23c622d

Pursey, Joanna Patricia (2017) Chemically tagged DNA probes for sensing of DNA biomarkers using Lab-on-a-chip technology. University of Southampton, Doctoral Thesis, 237pp.

Record type: Thesis (Doctoral)

Abstract

DNA methylation is a common epigenetic abnormality found in cancer. Although a high content of DNA methylation is found in cancer patients, the amount is still very low and multiple round of amplification is necessary. In addition, multiple genes are methylated in cancer patients. Therefore a high sensitivity and multiplexed sensor is desired for methylated DNA detection. This work develops a single sensor device and a multi sensor device multiplex work. To show the capability of these devices, bladder cancer biomarkers are selected for demonstration. In bladder cancer, three genes (DAPK, E. Cadherin and RARβ) are found to be methylated in the promoter region. A hairpin probe was designed with a redox active chemical tag incorporated into the design. Anthraquinone and porphyrin modified DNA probes were synthesised and compared with the commercially available methylene blue. Simultaneous detection of these three genes is essential for bladder cancer diagnosis. This work shows that with the multi sensor device, all three biomarkers can be detected in single run using only 20 minutes operational time, with a limit of detection of 250 fM.

Alongside detection of DNA methylation, an additional biomarker found in bladder cancer patients, microRNA, was investigated. Hairpin and linear probe designs were compared. The miRNA was detected in spiked Surine (urine negative control) to demonstrate the feasibility of the system with detection in human samples.

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Joanna Pursey Thesis - Version of Record
Available under License University of Southampton Thesis Licence.
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Published date: November 2017

Identifiers

Local EPrints ID: 417810
URI: http://eprints.soton.ac.uk/id/eprint/417810
PURE UUID: bbf8748d-cb65-4198-8469-9c10876ec0e1
ORCID for Eugen Stulz: ORCID iD orcid.org/0000-0002-5302-2276

Catalogue record

Date deposited: 14 Feb 2018 17:30
Last modified: 20 Nov 2020 05:01

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Contributors

Author: Joanna Patricia Pursey
Thesis advisor: Eugen Stulz ORCID iD

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