Assessment of Cost-Efficient Thermocycler Prototype for Polymerase Chain Reaction and Loop-Mediated Isothermal Amplification

Abstract

DNA amplification-based diagnostic is the most accurate method among others, especially during the COVID-19 pandemic. Thus, increasing the global demand for instrumentation and amplification reagents locally, hence increasing import. It is a worrying state in terms of logistics and the future domestic market. An effort for domestic production is a must. Previously a cost-efficient thermocycler prototype using Raspberry Pi and Phyton coding is constructed. Thermocycler prototype flow measurement and heat distribution have previously been tested but never put on a real test for DNA amplification diagnostic. This research aims to compare thermocycler prototypes and commercial for in two types of DNA amplification reactions, polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP). PCR is the most and more common method than LAMP, with the main difference of PCR require thermal cycling and LAMP operate in isothermal conditions. LAMP has a quicker reaction time and operates at a lower temperature. DNA pol with high strand displacement activity is used for LAMP, in this research Bsm pol is used for LAMP and Taq pol for PCR. Since the prototype thermocycler is designed to be as simple and inexpensive as possible for ease of manufacture and accessibility for every layer of society. Hence, its heat control and stability are not as good as a commercial thermocycler, with huge temperature fluctuation resonance from its set-point. That causes prototype incapability of performing PCR, no DNA band at 250-500 bp range in gel electrophoresis. However, the prototype is capable of performing LAMP, existing

Keywords

• dna amplification-based diagnostic, thermocycler prototype, polymerase chain reaction (pcr), and loop-mediated isothermal amplification (lamp)