Isolation of nucleic acids using silicon dioxide powder as a tool for environmental monitoring

Abstract

Isolation and purification of nucleic acids are basic laboratory procedures used in molecular analysis supporting determination of organisms in environmental monitoring. However, many different methods of isolation are commonly used, often being designed for a particular type of DNA extraction. While researchers commonly decide on commercial isolation kits for their ease of use and efficiency, they require large amounts of studied tissue, and the cost of purchasing such kits over a long run can be high. To provide an alternative to using commercial kits, we have developed a simple, rapid, cost-effective, and reliable protocol for DNA isolation from cultured fungi on slants and from dried fungal samples using silica particles (silicon dioxide powder) in chaotropic conditions. With the presented method, it is possible to isolate good-quality DNA from fungi in less than 1.5 h, using easily accessible chemicals. Compared with other methods employing CTAB or commercial kits, it allows fast, easy, and cheap DNA purification from two main sources of fungi routinely used for research. In addition to the method protocol, we also provide advice for further optimization of the isolation process to account for specific conditions, making the procedure more useful.