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

Jacek Urbaniak,Brayan Jacewski,Daniel Janowski

doi:10.1007/s10661-019-7840-2

Jacek Urbaniak, Brayan Jacewski + Show 1 more

Open Access

https://doi.org/10.1007/s10661-019-7840-2

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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.

Highlights

In different areas of environmental monitoring, when working with genera and species, there is still a risk of incorrect determination of the organisms and to provide monitoring of invasive or potentially risky species (Pusz et al 2017)
The method based on silicon dioxide particles was developed for routine isolation of nucleic acids (Boom et al 1990), later adapted for research on viruses (Malinowski 1997) and improved for detection of a viral pathogen in potato tissue extract (Zacharzewska et al 2014)
We provide a comparison of all used techniques, including commercially available DNA isolation kits

Summary

Introduction

In different areas of environmental monitoring, when working with genera and species, there is still a risk of incorrect determination of the organisms and to provide monitoring of invasive or potentially risky species (Pusz et al 2017). Morphological criteria are sometimes not well met by traditional approaches, including identification based on organism morphology (Darling and Blum 2007), and are insufficient in mycology, especially when microscopic fungi need to be determined. A fast and easy determination based on DNA tools has one critical step: the nucleic acid extraction, which has to be done fast, and cheaply. The extraction, from different materials like plants, fungi, or animal tissue, is a routinely performed method in every type of molecular analysis and research area: phylogenetic analysis, fingerprinting, or molecular cloning. Numerous commercial methods based on the use of silica columns or magnetic beads for nucleic acid purification have been developed, other methods, such as numerous variants of the CTAB extraction, are widespread and still used (Cheng et al 2003; Werth et al 2016).

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