Structural optimization for heat detection of DNA thermosequencing platform using finite element analysis |
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| Authors: | Hesaam Esfandyarpour Bo Zheng R Fabian W Pease and Ronald W Davis |
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| Institution: | 1Department of Electrical Engineering, Stanford University, Palo Alto, California 94305, USA;2Stanford Genome Technology Center, Palo Alto, California 94304, USA;3Department of Management Science and Engineering, Stanford University, Palo Alto, California 94305, USA;4Department of Genetics, Stanford University, Palo Alto, California 94305, USA;5Department of Biochemistry, Stanford University, Palo Alto, California 94305, USA |
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| Abstract: | For the past three decades, Sanger’s method has been the primary DNA sequencing technology; however, inherent limitations in cost and complexity have limited its usage in personalized medicine and ecological studies. A new technology called “thermosequencing” can potentially reduce both the cost and complexity of DNA sequencing by using a microfluidic platform Esfandyarpour, Pease, and Davis, J. Vac. Sci. Technol. B26, 661 (2008)]. To optimize the efficiency of the technology, finite element analysis was used to model the thermosequencing system by simulating the DNA incorporation reaction series and the resulting product concentration and heat production. Different models of the thermosequencing platform were created to simulate the effects of the materials surrounding the system, to optimize the geometry of the system, and to concentrate reaction heat into specific regions for detection in the real system. The resulting concentrations of reaction products were used to calibrate the reaction speed and to design the heat sensors in the thermosequencing technology. We recommend a modified gated structure for the microfluidic detection platform by using control valves and show how this new platform could dramatically improve the detection efficiency. |
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