Increasing Purity of Extracted DNA from Young Oak Leaves

Ryan Brooks.

Published May 2026 in International Oaks No. 37: 107–114

Abstract

Oaks are well known for the abundance of secondary metabolites present in their tissues. These chemicals serve many ecological functions, but are also a major factor in this group’s economic importance. Tannins, more specifically, can be used for tanning leather, flavoring wines and whiskeys, or medicinally. Despite their many uses, tannins create challenges when isolating and purifying DNA due to their high affinity for negatively charged molecules, like the nucleotides that make up DNA. This leads to DNA samples often being contaminated with phenolic compounds, inhibiting downstream techniques, such as PCR, that aim to analyze the sample. Extraction of DNA from oak tissues is commonly done using commercial extraction kits, however these can produce very low yields of purified DNA, which is problematic when starting with small amounts of valuable tissue from threatened species. In order to get around these challenges, we leveraged tannin leaching techniques used in other applications to remove tannins prior to extracting and purifying nuclear DNA using a standard CTAB protocol. This project explores which existing tannin extraction methods can be implemented to reach the highest level of tannin removal without compromising the quality of nuclear DNA from young leaf tissue. The best results are from samples that are heated while submerged in a basic solution that is periodically replaced. This method has produced DNA suitable for PCR amplification and that meets quality standards for next generation sequencing.

Keywords

ex-situ conservation, conservation genetics, tissue culture, cryopreservation, somatic mutation, somaclonal variation, threatened

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