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Design and Fabrication of an Integrated Lab-on-a-chip System for DNA Extraction from Cells and Gene Amplification

Topa Heidari, Mohammad Mahdi | 2025

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 58102 (08)
  4. University: Sharif University of Technology
  5. Department: Mechanical Engineering
  6. Advisor(s): Shamloo, Amir; Nouri Borujerdi, Ali
  7. Abstract:
  8. In this study, an integrated lab-on-a-chip (LOC) system was designed and developed to perform various processes, including cell separation, cell lysis, DNA extraction, and amplification, in an automated and unified manner. The system was designed to operate with fully disposable components, eliminating the risk of cross-contamination. The design includes five distinct microfluidic chips, each dedicated to a specific function. For cell separation, the inertial method was employed, which operates without the need for a micromixer and delivers high accuracy. Simulations demonstrated a recovery rate of 100% and a purity of 96.8%, while experimental results showed a recovery rate of 88.8% and a purity of 83.7%. Additionally, surrogate modeling was utilized to investigate different cancer cell types and optimize the aspect ratio parameter. The findings revealed that an optimal aspect ratio of 0.2 in the designed microchannel significantly enhanced separation performance, achieving a recovery rate of 100% and a purity of over 97% for circulating tumor cells (CTCs) larger than 20 µm in diameter. Cell lysis was carried out using a chemical lysis method and a controlled heating module. DNA extraction was optimized using a silica filter and precise fluid flow control through a cylindrical rod design operated by a servo motor. A comparison of extraction results indicated that the device achieved an efficiency of 10.21% relative to the standard method, producing DNA suitable for molecular applications. Following DNA extraction, polymerase chain reaction (PCR) was performed, and the resulting products were evaluated for quantity using agarose gel electrophoresis. Both extraction methods produced DNA of sufficient quality for PCR, as evidenced by clear bands of the target gene in the electrophoresis results. Additionally, the quality and expression of the gene were assessed using Real-Time PCR, which confirmed successful amplification and high-quality samples. These findings validate the accuracy of the gene amplification process and its successful expression. With its efficient and innovative design, this system enables rapid preparation of DNA samples for biotechnological studies and medical diagnostics
  9. Keywords:
  10. Lab-on-a-Chip ; Cell Separation ; DNA Extraction ; Gene Amplification ; Microfluidic System ; Chemical Cell Lysis ; Disposable System ; DNA Amplification

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