Design, Simulation and Construction of a Rapid Gene Amplification Microfluidic Device Using Polymerase Chain Reaction (PCR) Method

Amadeh, Ali | 2018

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 51689 (08)
  4. University: Sharif University of Technology
  5. Department: Mechanical Engineering
  6. Advisor(s): Shamloo, Amir
  7. Abstract:
  8. Polymerase chain reaction method is a conventional method for obtaining multiple copies of a specified segment in the DNA molecule and to amplify the DNA molecule itself. Therefore, this method has been of paramount importance in different fields of research and has been applied for different applications. PCR requires thermal cycling, or repeated temperature changes between two or three discrete temperatures to amplify specific nucleic acid target sequences. To achieve such thermal cycling, conventional bench-top thermal cyclers generally use a metal heating block powered by Peltier elements or benefit from forced convection heat transfer. Although efforts have been made in order to reduce the time needed for DNA amplification using these methods, they are still time-consuming. Thus, it seems that design and fabrication of a fast/ultrafast PCR can be definitely useful for genomic testing at the point-of-care (POC) level in which the test itself, obtaining the results, and their analysis must be done as soon as possible. In this piece of research, a microfluidic PCR system has been proposed which benefits from plasmonic photothermal heating for thermal cycling. The results show that the heating and cooling rates for 35 µl volume of the sample (consisting of 15 µl mineral oil and 20 µl template) are 5 °C/s and 3 °C/s, respectively. Considering the energy consumption of the proposed system, which uses only a 10 W LED for heating the sample, one can easily understand the efficiency of such a method for this purpose. The proposed protocol for amplifying the target DNA is suitable due to the results of the gel-electrophoresis test which bears witness to the fact that the system is able to amplify the sample perfectly. Moreover, this protocol is repeatable for our system. The ongoing research is focused on fabricating a centrifugal PCR system which utilizes the aforementioned method for thermal cycling. According to the simulations done, an angular speed of about 20 Hz can yield a suitable performance for the designed system
  9. Keywords:
  10. Polymerase Chain Reaction (PCR) ; Thermal Cycle ; Plasmonic Photothermal Heating ; Centrifugal Microfluidics ; DNA Molecule

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