Model microfluidic platform prototyping : design and fabrication of a Polymerase Chain Reaction (PCR) chip

Abstract

Polymerase Chain Reaction (PCR) is a molecular biology method for the in vitro amplification of nucleic acid molecules, which has wide applications in the areas of genetics, medicine and biochemistry. MEMS technology offers several advantages for the miniaturization of biological protocols like PCR, including decreased amplification time, reduced reagent consumption, disposability, target specific amplification, and functional integration. The typical three step PCR cycle consists of heating the sample to 90-95 °C to denature the double-stranded DNA complex, cooling down to 55-60 °C to anneal the specific primers to the single stranded DNA, and finally increasing the temperature to 70-75 °C for extension of the primers with thermostable DNA polymerase. The temperature sensitivity of the reaction requires precise temperature control and proper thermal isolation of the three temperature zones. In this thesis, the design of a continuous flow PCR microfluidic platform consisting of a monolithic polydimethylsiloxane (PDMS) microfluidic chip assembled on top of a thin film patterned glass base heating unit is presented. A detailed thermo-fluidic model of the device is presented to predict the performance and efficacy of the proposed design. Numerical simulations are carried out to find the temperature distribution in the device and show the suitability of the design in meeting target temperature profile. Subsequently, simulation results are substantiated with experimental results of infrared and thermocouple temperature measurement on the device.

(cont.) An instrumented microfluidic platform was developed and experiments were carried out to investigate amplification efficiency. Different vapor barrier mechanisms and channel coatings were explored for minimizing sample loss. The research presented is an effort towards developing miniaturized, cost-effective, portable platform capable of replacing conventional thermocyclers.