Validation of a simplified small-scale DNA extraction protocol from wine by quantitative real-time PCR

TL;DR

The study validates a simplified DNA extraction method from wine, showing it produces high-quality DNA suitable for PCR.

Contribution

A simplified small-scale DNA extraction protocol for wine is validated as effective and inhibitor-free.

Findings

The simplified DNA extraction method from wine is effective and produces DNA free of PCR inhibitors.

DNA extracted from wine is qualitatively equivalent to DNA from grapevine leaves.

Two nuclear genes were successfully amplified from wine-derived DNA using real-time PCR.

Abstract

In the present study, we compared a simplified small-scale purification protocol to obtain DNA admixtures out of wine, with our large-scale published method. The extraction methods must provide DNA free of PCR inhibitors, that can interfere with DNA amplification. To evaluate the efficiency of grapevine’s nuclear DNA extraction from wine, the new protocol was also compared in terms of purity and yield to the DNA obtained out of grapevine’s (Vitis vinifera) leaf tissue, using a commercial kit. Two single-copy nuclear genes, nine-cis-epoxy carotenoid dioxygenase 2 (NCED2), and prefoldin subunit 5-like (PS5) were amplified in DNA extracted from wine and grapevine by real-time TaqMan PCR to determine the presence of inhibitors in relation to the diversity of starting biological matrix. This study showed that the small-scale, simpler method for extracting DNA from wine produced effective results in terms of inhibitor presence and purity. Furthermore, even though the initial biological matrix was more complicated, the grapevine nuclear DNA that was removed from wine was qualitatively equivalent to the DNA that was isolated from the leaves.

The online version contains supplementary material available at 10.1007/s13205-024-03992-x.

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