Comparative Evaluation of CTAB and AP1 Buffers in On-Chip DNA Extraction of Pathogenic Fungus for Microfluidic Interdigitated-Electrode Biosensing

Abstract

Conventional methods such as tissue culture and PCR-based analyses are expensive and time-consuming, often requiring up to two weeks and intensive labor. In contrast, microfluidic lab-on-a-chip systems provide much faster detection (roughly an hour), reduce costs, and require only minimal sample volumes. This study presents a streamlined PDMS microfluidic workflow for on-chip DNA extraction and label-free detection of Ganoderma boninense, a pathogenic fungus that majorly impacts palm oil plantations in Malaysia. We compared two lysis buffers, CTAB and AP1, to evaluate DNA yield and purity. UV-Vis analysis indicated that AP1 consistently resulted in higher DNA concentrations, while CTAB extracts exhibited smoother absorbance spectra, suggesting lower levels of impurities. In addition to that, the expected peak near 260 nm was observed with additional shoulders around 280–290 nm across extracts, which are characteristic of both dsDNA and ssDNA, demonstrating successful DNA extraction on the microfluidics chip. Electrical I-V measurements using the AuNP-ZnO-coated IDE biosensor revealed increased DNA hybridization signals, confirming both extraction and detection processes were successful. Overall, AP1 produced a much higher DNA recovery (albeit with increased background absorbance), whereas CTAB yielded ‘purer’ DNA. This integrated microfluidic system enables rapid and sensitive detection of G. boninense, demonstrating its potential for field-based diagnostic applications.