Multidisciplinary Design and Optimization for Oscillating Flow Polymerase Chain Reaction Microfluidics Device

Abstract

A Polymerase Chain Reaction (PCR) process is almost always required prior to DNA (deoxyribonucleic acid) analysis to create multiple copies of DNA fragments. Using microfluidics technology, the PCR process requires much shorter process time and much less DNA samples than conventional PCR systems. Among existing microfluidics-based techniques, the oscillating flow PCR has advantages including faster analysis time than cavity PCR microfluidics, and smaller contact area between the sample and polymer channel wall compared to flow-through PCR. The smaller contact area reduces DNA adsorption and enhances DNA detection accuracy. In the proposed study, new design features of the oscillating flow PCR concept are evaluated including: (1) PDMS (polydimethylsiloxane) and glass are selected as the microfluidics chip material for realizing a disposable chip, (2) water impingement cooling is applied to effectively isolate the temperature zones, and (3) a copper layer is attached outside of the chip to enhance uniform temperature distribution within the temperature zones. When PDMS is used for PCR microfluidics devices, lower efficiency has been a disadvantage. The efficiency is lowered because the DNA fragments are trapped at the PDMS surface. This trapping can be reduced by minimizing the contact area between the sample and the PDMS surface. When the sample contact area is reduced, which can be achieved by increasing the flow channel cross-sectional area, thermal response is degraded. Optimal channel dimensions are determined by considering the trade-off between thermal response and sample contact area with PDMS channel wall. The resulting thermal response of the sample in the temperature zone is comparable to existing studies, which use silicon as the chip material. A transient FEM heat transfer analysis for the temperature zone is performed for more effective thermal design and optimization.