Design of a low-cost real-time PCR machine

Author: Lingchen Wang

Wang, Lingchen, 2021 Design of a low-cost real-time PCR machine, Flinders University, College of Science and Engineering

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Introduction: Polymerase chain reaction (PCR) is an important tool for DNA profiling in forensic science. The PCR machine can generate millions/billions of targeted DNA copies with only several copies to start. However, the process of PCR is almost fixed since it was discovered in the 1980s. We believe that we can add a sensor to the PCR to monitor the process, and test whether we can apply machine learning to the PCR machine to improve the PCR behaviour. The optimised PCR process might reduce time duration and increase specificity which leads to the increased efficiency of PCR and save money.

Aim: The first half of the aim of this thesis is to design a low-cost optical system that can quantify the DNA concentration of the PCR sample in real-time; the second half is to design a real-time PCR machine that uses the optical system.

Methodology and result: We have designed an optical system that can measure the concentration of DNA within a PCR product that contains fluorescence dye. The experiment uses a blue LED as the light resource and a spectrometer to detect the percentage ratio between the green and blue light from the sample. The result shows that both Green/Blue (%) and the green light intensity increase as the DNA concentration increases.

Discussion and conclusion: Our design is able is distinguish PCR products with different concentrations; however, a minimum loading volume is required to conduct a valid measurement. The future work includes experiments with more samples to complete the conversion between the fraction and DNA concentration and upgrading an open-source PCR machine to a qPCR machine (also called real-time PCR) which measures the quantification of the PCR process in real-time. Future experiments with the PCR parameters can be conducted to sketch the machine learning algorithm for PCR process optimisation.

Keywords: Polymerase chain reaction (PCR), qPCR, open-source, DNA quantification, spectrometer, optical system

Subject: Engineering thesis

Thesis type: Masters
Completed: 2021
School: College of Science and Engineering
Supervisor: Russell Brinkworth