Czech J. Food Sci., 2021, 39(5):410-417 | DOI: 10.17221/24/2021-CJFS

Comparison of methods to extract PCR-amplifiable DNA from fruit, herbal and black teasOriginal Paper

Eliška Čermáková ORCID...*,1, Kamila Zdeňková1, Kateřina Demnerová1, Jaroslava Ovesná2
1 Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Prague, Czech Republic
2 Crop Research Institute, Prague, Czech Republic

The success of polymerase chain reaction (PCR) assay depends on template deoxyribonucleic acid (DNA) being sufficient with respect to both quantity and quality. Some biological materials contain compounds which inhibit the functioning of DNA polymerase and thus need to be removed as part of the DNA extraction procedure. The aim of the present experiments was to optimise the process of DNA isolation from various types of black, fruit and herbal teas. A comparison was made between two cetyltrimethylammonium bromide (CTAB)-based protocols and two commercially available DNA purification kits. The yield and integrity of the extracted DNA were monitored both spectrophotometrically and using agarose gel electrophoresis. The presence/absence of inhibitors in the DNA preparations was checked by running quantitative real-time PCRs. The optimal protocol was deemed to be the CTAB method described in ISO 21571:2005, so this method is recommended for the routine sample analysis of tea products.

Keywords: CTAB; DNA extraction; PCR amplification; tea; tRNA-Leu

Published: October 14, 2021  Show citation

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Čermáková E, Zdeňková K, Demnerová K, Ovesná J. Comparison of methods to extract PCR-amplifiable DNA from fruit, herbal and black teas. Czech J. Food Sci. 2021;39(5):410-417. doi: 10.17221/24/2021-CJFS.
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    References

    1. Akkurt M. (2012): Comparison between modified DNA extraction protocols and commercial isolation kits in grapevine (Vitis vinifera L.). Genetics and Molecular Research, 11: 2343-2351. Go to original source... Go to PubMed...
    2. Attitalla I.H. (2011): Modified CTAB method for high quality genomic DNA extraction from medicinal plants. Pakistan Journal of Biological Sciences, 14: 998-999. Go to original source...
    3. Bernardo G.D., Gaudio S.D., Galderisi U., Cascino A., Cipollaro M. (2007): Comparative evaluation of different DNA extraction procedures from food samples. Biotechnology Progress, 23: 297-301. Go to original source... Go to PubMed...
    4. Cota-Sánchez J.H., Remarchuk K., Ubayasena K. (2006): Ready-to-use DNA extracted with a CTAB method adapted for herbarium specimens and mucilaginous plant tissue. Plant Molecular Biology Reporter, 24: 161-167. Go to original source...
    5. Csaikl U., Bastian H., Brettschneider R., Gauch S., Meir A., Schauerte M., Scholz F., Sperisen C., Vornam B., Ziegenhagen B. (1998): Comparative analysis of different DNA extraction protocols: A fast, universal maxi-preparation of high quality plant DNA for genetic evaluation and phylogenetic studies. Plant Molecular Biology Reporter, 16: 69-86. Go to original source...
    6. Dellaporta S.L., Wood J., Hicks J.B. (1983): A plant DNA minipreparation: Version II. Plant Molecular Biology Reporter, 1: 19-21. Go to original source...
    7. Demeke T., Jenkins G.R. (2010): Influence of DNA extraction methods, PCR inhibitors and quantification methods on real-time PCR assay of biotechnology-derived traits. Analytical and Bioanalytical Chemistry, 396: 1977-1990. Go to original source... Go to PubMed...
    8. Dimitrijević A., Pejović I., Imerovski I., Dedić B., Pajević S., Miladinović D. (2013): DNA isolation from dry samples of broomrape - The effect of isolation method and sample storage on DNA yield and quality. Romanian Agricultural Research, 30: 349-357.
    9. Doyle J.J., Doyle J.L. (1990): Isolation of plant DNA from fresh tissue. Focus, 12: 39-40.
    10. Efenberger-Szmechtyk M., Nowak A., Kregiel D. (2018): Implementation of chemometrics in quality evaluation of food and beverages. Critical Reviews in Food Science and Nutrition, 58: 1747-1766. Go to original source... Go to PubMed...
    11. European Network of GMO Laboratories (2011): Verification of analytical methods for GMO testing when implementing interlaboratory validated methods. Joint Research Centre (JRC) Scientific and Technical Reports. Luxembourg, Publications Office of the European Union: 1-23.
    12. Gaikwad A.B. (2002): DNA extraction: Comparison of methodologies. PLoS Biology, 20: 162-173.
    13. Granato D., Putnik P., Kovačević D.B., Santos J.S., Calado V., Rocha R.S., Cruz A.G.D., Jarvis B., Rodionova O.Y., Pomerantsev A. (2018): Trends in chemometrics: Food authentication, microbiology, and effects of processing. Comprehensive Reviews in Food Science and Food Safety, 17: 663-677. Go to original source... Go to PubMed...
    14. Gryson N. (2010): Effect of food processing on plant DNA degradation and PCR-based GMO analysis: A review. Analytical and Bioanalytical Chemistry, 396: 2003-2022. Go to original source... Go to PubMed...
    15. Hrbek V., Rektorisova M., Chmelarova H., Ovesna J., Hajslova J. (2018): Authenticity assessment of garlic using a metabolomic approach based on high resolution mass spectrometry. Journal of Food Composition and Analysis, 67: 19-28. Go to original source...
    16. Hrnčírová Z., Bergerová E., Siekel P. (2008): Effects of technological treatment on DNA degradation in selected food matrices of plant origin. Journal of Food & Nutrition Research, 47: 23-28.
    17. Karni M., Zidon D., Polak P., Zalevsky Z., Shefi O. (2013): Thermal degradation of DNA. DNA and Cell Biology, 32: 298-301. Go to original source... Go to PubMed...
    18. Li Q., Mei J., Zhang Y., Li J., Ge X., Li Z., Qian W. (2013): A large-scale introgression of genomic components of Brassica rapa into B. napus by the bridge of hexaploid derived from hybridization between B. napus and B. oleracea. Theoretical and Applied Genetics, 126: 2073-2080. Go to original source... Go to PubMed...
    19. Lodhi M.A., Ye G.N., Weeden N.F., Reisch B.I. (1994): A simple and efficient method for DNA extraction from grapevine cultivars and Vitis species. Plant Molecular Biology Reporter, 12: 6-13. Go to original source...
    20. McGrath T.F., Haughey S.A., Patterson J., Fauhl-Hassek C., Donarski J., Alewijn M., van Ruth S., Elliott C.T. (2018): What are the scientific challenges in moving from targeted to non-targeted methods for food fraud testing and how can they be addressed? - Spectroscopy case study. Trends in Food Science & Technology, 76: 38-55. Go to original source...
    21. Park K.W., Lee B., Kim C.G., Park J.Y., Ko E.M., Jeong S.C., Choi K.H., Yoon W.K., Kim H.M. (2010): Monitoring the occurrence of genetically modified maize at a grain receiving port and along transportation routes in the Republic of Korea. Food Control, 21: 456-461. Go to original source...
    22. Peano C., Samson M.C., Palmieri L., Gulli M., Marmiroli N. (2004): Qualitative and quantitative evaluation of the genomic DNA extracted from GMO and non-GMO foodstuffs with four different extraction methods. Journal of Agricultural and Food Chemistry, 52: 6962-6968. Go to original source... Go to PubMed...
    23. Porebski S., Bailey L.G., Baum B.R. (1997): Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Molecular Biology Reporter, 15: 8-15. Go to original source...
    24. Sajali N., Wong S.C., Hanapi U.K., Suhaili Abu Bakar J., Tasrip N.A., Mohd Desa M.N. (2018): The challenges of DNA extraction in different assorted food matrices: A review. Journal of Food Science, 83: 2409-2414. Go to original source... Go to PubMed...
    25. Sharma P., Purohit S. (2012): An improved method of DNA isolation from polysaccharide rich leaves of Boswellia serrata Roxb. Indian Journal of Biotechnology, 11: 67-71.
    26. Sovová T., Křížová B., Ovesná J. (2018): Determining the optimal method for DNA isolation from fruit jams. Czech Journal of Food Sciences, 36: 126-132. Go to original source...
    27. Taberlet P., Gielly L., Pautou G., Bouvet J. (1991): Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology, 17: 1105-1109. Go to original source... Go to PubMed...
    28. Valter K. (2010). Everything About Tea for Tea Lovers (Vše o čaji pro čajomily). Prague, Czech Republic, Granit: 191. (in Czech)
    29. Wilfinger W.W., Mackey K., Chomczynski P. (1997): Effect of pH and ionic strength on the spectrophotometric assessment of nucleic acid purity. Biotechniques, 22: 474-481. Go to original source... Go to PubMed...
    30. Xanthopoulou A., Ganopoulos I., Kalivas A., Osathanunkul M., Chatzopoulou P., Tsaftaris A., Madesis P. (2016): Multiplex HRM analysis as a tool for rapid molecular authentication of nine herbal teas. Food Control, 60: 113-116. Go to original source...

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