EFFICIENCY OF DIFFERENT METHODS OF EXTRACTION OF DNA SUITABLE FOR PCR FROM HERBAL SPECIMENS OF ALGAE GENUS CLADOPHORA KÜTZ.

А. О. Bakuma, T. G. Alieksieieva, F. P. Tkachenko

Abstract


DNA extraction from algae presents unique challenges due to the production of various polysaccharides and polyphenols, which can act as PCR inhibitors. Consequently, optimizing DNA extraction methods becomes necessary for different groups of algae. The Cladophora genus, known for its high morphological variability influenced by environmental conditions and developmental stages, can benefit from molecular genetic analysis in addressing taxonomic and phylogenetic inquiries within the green algae family.
In this context, the primary objective of this study was to select an appropriate DNA extraction method for herbarium specimens of Cladophora algae and evaluate the extracted DNA's suitability for PCR. The study compared two DNA extraction methods, namely the SureFood PREP Basic kit from R-Biopharm and the Quick DNA Mini Prep kit from Zymo Research. Subsequently, the isolated DNA was subjected to PCR using the universal primer iPBS 2080 with different reaction mixtures containing Dream-Taq polymerase and Sso7d DNA polymerase.
The results revealed that the DNA concentrations and purification rates obtained from samples extracted using the SureFood PREP Basic kit were notably superior. However, PCR using these DNA samples did not yield positive results, likely due to the presence of inhibitors. On the other hand, DNA extracted using the Quick DNA Mini Prep kit exhibited lower purification rates but likely contained fewer DNA polymerase inhibitors. This allowed for successful amplification with the iPBS 2080 primer, utilizing the high-efficiency Sso7d polymerase, known for its resistance to inhibitors.

Keywords


Cladophora; DNA extraction; PCR; molecular markers; molecular-genetic analysis; polymorphism

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DOI: https://doi.org/10.25128/2078-2357.23.1-2.5

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