Ultrasonication as a rapid and high yield DNA extraction method for bacterial gene quantification by NanoGene assay

We demonstrated ultrasonication as a rapid and high yield DNA extraction method suitable for bacterial gene quantification by NanoGene assay. The NanoGene assay utilizes DNA hybridization in solution and a combination of magnetic beads and quantum dot nanoparticles. Unlike the existing gene quantification assays, the NanoGene method is capable of quantifying genes in the presence of environmental inhibitors and cell materials. The performance of the ultrasonication was compared with heating and freeze-thaw. They first were evaluated for their cell lysis capability in humic acids laden sand samples, via EtBr assay. Using autoclaved samples as a bench mark, their cell lysis capability were 106 ± 3, 68 ± 5, and 48 ± 15%, respectively. Morphological changes of cells for each method were also observed by FE-SEM. More importantly, ultrasonication performed significantly better (more than 3× fluorescence signal) than commercial DNA extraction methods during bacterial gene quantification in humic acids laden sand samples.