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

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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Identifiers

ORCID for Eugen Stulz: orcid.org/0000-0002-5302-2276

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