Design and implementation of micro temperature cycler for polymerase chain reaction

Miniaturization of biological and chemical analytical devices with microelectromechanical systems (MEMS) technology has been important for medical and microbiological diagnostics and other biological analyses. Existing or emerging infectious diseases are increasing the need for point-of-care (POC) testing to improve timely diagnosis. Traditional methods for nucleic acid detection require many steps. Some of these technologies can be highly sensitive. However, it lags behind in developing POC devices due to low detection limits, time and instrumentation requirements. To overcome these challenges, microfluidic technologies are used that allow all analytical steps, including sample pretreatment, reactions, separations, and diagnostics, to be performed efficiently and automatically in microchannels on a small chip. Polymerase chain reaction (PCR), one of the nucleic acid amplification methods, has become the most used method due to its simplicity. Microfluidic technologies enable the miniaturization of PCR processes on a chip with potential benefits such as speed, cost, portability, efficiency and automation. With the thesis study, the design and production of the microchip and micro temperature cycler required to perform PCR were carried out. For this purpose, Computer Aided Design (CAD) program was used in the microchip design, and a laser cutter, one of the CAD methods, was used in its production and a single-chamber chip was produced. The materials used in microchip production were coverslips, double-sided tape (DSA) and polymethylmethacrylate (PMMA) polymer. Peltier module was chosen as the heating element to be used in the production of micro temperature cycler. Microcontroller and H-Bridge modules were used to perform temperature control. Temperature cycler circuit analysis was first made in a simulation program and the PCR cycle could be performed. Then, appropriate elements were provided to implement this circuit. The modes of H bridge type drivers and the circuit mechanisms regarding how they are driven with a microcontroller have been studied. H-bridge driving (with the help of a microcontroller) has been tried with the pulse width modulation (PWM) technique, which is one of the motor driving techniques. Firstly, Peltier module temperature tests were carried out with the supplied elements. The PCR cycle was realized by combining the circuit elements whose suitability was tested with the PID control algorithm developed for temperature cycle control. A different CAD program was used to simulate heat transfer and fluid flow. This software is based on the finite-element method. It makes it easy to combine and solve partial differential equations from different fields of physics. Laminar flow was simulated within the microchip using the fluid flow module. Additionally, an attempt was made to simulate the heat transfer in chip materials by using the heat transfer module. The DNA sample was amplified with the designed micro temperature cycler at Kırıkkale University Faculty of Medicine, Department of Medical Biology. To test that the design performed PCR, the sample used on the temperature cycler was also amplified using a commercial temperature cycler and the results were then determined with an appropriate analysis method.