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The determination of olive oil quality using molecular tools is mainly based on the extraction and obtaining of DNA in sufficient quantity and quality. However, this task faces several difficulties and obstacles, including the presence of nucleases in olive oil that cause DNA degradation, but also phenolic compounds and polysaccharides that inhibit the activity of DNA polymerase during PCR reactions, in addition to the storage time of samples that also affects the quality of residual DNA. In this synthesis, we try to review the different attempts and techniques to obtain residual DNA, before ending with the description of the protocol we propose.