Development of a MEMS-based microfluidic electrochemical biosensor for the detection of circulating tumor DNA

Date

2025-5-26

Author

Çağlayan Arslan, Zeynep

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Recent advances in microfluidic biosensors have significantly enhanced the analytical performance of diagnostic platforms, particularly for cancer biomarker detection. Among these, electrochemical biosensors are widely preferred due to their ease of miniaturization, low cost, and compatibility with microfluidic integration, making them highly suitable for point-of-care applications. These advantages are especially valuable in liquid biopsy approaches, where circulating tumor DNA (ctDNA) offers a non-invasive alternative to traditional tissue biopsies. In hepatocellular carcinoma (HCC), a highly heterogeneous and aggressive liver cancer, ctDNA provides crucial molecular information that conventional biopsies often fail to capture. In this thesis, a label-free and pre-enrichment-free electrochemical biosensor based on microfluidics and MEMS technologies was developed for the sensitive detection of ctDNA associated with HCC. Prior to integrating the sensor system with microfluidics, a MEMS-based planar electrochemical biosensor platform—operated under static conditions and utilizing the same three-electrode configuration—was used to systematically optimize surface functionalization and hybridization conditions. These optimization studies guided the experimental workflow applied to the final microfluidic biosensor, which was fabricated with a three-electrode configuration (Au working, Pt counter, and Ag reference electrodes) on a glass substrate, patterned via photolithography and metal lift-off processes, and integrated with a PDMS microchannel for fluidic operation. Thiolated single-stranded DNA probes were immobilized on the gold working electrode to enable hybridization-based recognition of ctDNA targets. Electrochemical impedance spectroscopy (EIS) was used to monitor these hybridization events, eliminating the need for amplification or labeling. The finalized microfluidic platform achieved a limit of detection (LOD) of 1.43 fM within a 2–200 fM dynamic range. High specificity was confirmed through mismatch studies using one-base mismatched and fully non-complementary sequences. This study presents the first MEMS-based microfluidic electrochemical biosensor tailored for ctDNA detection in HCC, combining sensitivity, specificity, and operational simplicity. The proposed platform demonstrates strong potential for adaptation in point-of-care diagnostics and precision oncology.

Subject Keywords

MEMS-based electrochemical biosensor, Microfluidics, Circulating tumor DNA (ctDNA), Hepatocellular carcinoma (HCC), Electrochemical impedance spectroscopy (EIS)

URI

https://hdl.handle.net/11511/115038

Collections

Graduate School of Natural and Applied Sciences, Thesis