Thermal Analysis of a Micro-Polymerase Chain Reaction Device

Abstract

Micro-scale polymerase chain reaction (micro-PCR) systems offer substantial advantages over macro-scale systems. Smaller sample volumes are required, and faster process times are feasible. Thermal control of micro-PCR systems is a substantial technical challenge, however. The PCR process requires the fluid sample to be cycled through three temperature ranges — typically 90–95°C, 50–65°C and 72–77°C for denaturation, hybridisation and replication respectively. Durations of the three steps are required to be in the ratio of 4:4:9. In this paper, the thermal analysis of a continuous flow micro-PCR device is reported. The objective of the analysis is to optimize the thermal performance of the device for fast amplification cycles with high efficiency - an efficient PCR features rapid heating and cooling between steps, and good temperature uniformity within each step. The device comprises an array of parallel microchannels formed within a polypropylene substrate to carry fluid, with the base of the substrate mounted on an aluminium carrier. Substrate depth is 500 micron, and each channel is 60 micron wide by 40 micron deep. Thermoelectric cells (TECs) are bonded to the carrier, and powered by a thermoelectric controller with feedback from sensors embedded in the carrier. A Pyrex Glass slide is bonded to the substrate to form closed channels. Arrays of film heaters mounted on the slide adjacent to the channel are used to establish the required temperature regions along the channel. By pumping the fluid at a fixed flow rate, temperature cycling of specific period is achieved. Thermal analysis of the substrate is performed using an approximate closed-form solution, in conjunction with Finite Element (FE) and Computational Fluid Dynamics (CFD) simulations. The analysis is used to conduct a parametric study in order to determine the optimum configurations of substrate materials, cooling conditions, heaters and flow rates required to impose specific temperature cycles. The use of thermoelectric cells is shown to increase the rate of change of temperature between the various regions, improving the efficiency and decreasing the cycle time of the PCR process. Cycle times of 6s or less are shown to be feasible, yielding benefits in time saved for multiple amplifications. Finally, the analysis is also used to identify the dimensionless parameters which govern the thermal characteristics of the device, illustrating the importance of the Biot number.