Design and Analysis of a Heat Conduction-Based Continuous Flow Polymerase Chain Reaction System

Abstract

Miniaturized ploymerase chain reaction (PCR) systems have attracted increasing interest in medicine and biology for its reduced sample volume and faster thermal cycling compared to conventional PCR device. The thermal cycling in a PCR device involves three temperatures: 95°C to 90°C for DNA denaturation, 50°C to 65°C for hybridization, and 72°C to 77°C for replication. In this work, a completely new concept of obtaining a temperature zone is presented, i.e., some temperature zone is not created by direct micro-heater heating, by natural heat conduction. Finite element method (FEM) is employed to analyze the temperature distribution in the new PCR designs. Three different designs were compared: (1) three heaters, (2) one heater, and (3) two heaters. For the three-heater design, the FEM simulation shows that large space must be reserved between heaters in order to avoid thermal cross-talking maintain a relatively uniform heating zone. For the single heater design, we have only one heater to reach 92 °C. Due to heat conduction, the temperature reduces gradually along the length of the device. We can setup the hybridization and replication zones at certain locations (along the direction of heat conduction) without using a micro-heater. The PCR device based on this design is easy to fabricate. But FEM simulation shows that the temperature gradient is about 8°C/ram. To overcome this “rapid” temperature gradient problem, we proposed to use two heaters. This design involves two heaters both sides. One heater is controlled to be 92°C for denaturation, and on the other end we use another heater set to 75°C for replication. The hybridization temperature (50 °C ∼ 65°C) is obtained from thermal conduction. In PCR operation, the time ratio for denaturation: hybridization: replication is about 4:4:9. For a continuous flow with a width of 80 μm and a depth of 30 μm and flow ranging from 5 nl/s to 80 nl/s, the 20-cycle PCR can be fabricated within an area of 56 mm × 28 mm area, which is smaller than previous design (Kopp et al., 1998). The length of the microchannel is about 0.6 m, which yields a cycling time from 22 seconds to 6 minutes.