Assessment of the cellulose-based dipstick method for bacterial and fungal DNA extraction

The development of rapid, low-cost DNA extraction methods is crucial for advancing molecular diagnostics and biological research. Conventional silica column-based kits, while efficient, are limited by cost, complexity, time, and equipment requirement, particularly in resource-limited settings. This study evaluates a cellulose-based dipstick method as a low-cost and fast alternative for DNA extraction form bacteria and fungi. Cellulose dipsticks, made of Whatman Grade 1 filter paper, were used in combination with optimized mechanical lysis protocols using glass beads in a sodium dodecyl sulfate (SDS) detergent-containing buffer solution. DNA yield, purity, and compatibility with quantitative PCR processes were carefully compared with commercially available silica columns for nine bacterial and five fungal species. The dipstick method yielded DNA concentrations of 0.94 ± 0.29 μg/mL for bacteria and 0.50 ± 0.15 μg/mL for fungi, with A260/A280 ratios of 1.73 ± 0.07 and 1.45 ± 0.24, respectively. Although the yield and purity were lower than those obtained with commercially available column-based extraction kit, the quantity and quality of DNA obtained using the dipstick method were sufficient for most PCR-based downstream applications. The dipstick method required just 30 ± 5 seconds to carry out the extractions compared to the 30 to 60 minutes required for commercially available DNA extraction kits. Agarose gel electrophoresis verified the integrity or the quality of the extracted DNA, with efficient amplification of target genes in all the species examined. The simplicity, rapidity, and field-friendly nature of the method readily circumvent significant issues with sample transport, stability of the samples during storage and transportation, and the cost of extraction. Nevertheless, the limitations of the dipstick DNA extraction method are its low DNA yield and the fragility of dipsticks during washing steps, which might limit suitability for high throughput applications. Despite these restrictions, the cellulose-based dipstick method offers a practical, scalable solution for DNA extraction in low-resource environments, with significant potential for field diagnostics and ecological studies.