Total Genomic DNA Extraction Studies from Seaweeds
Abstract
One of marine resources that has high value is seaweed. Seaweed is a carrageenan producer used in the food industry. Seaweed contains many minerals, vitamins and proteins that are useful for health. Carotenoids are pigments found in seaweed that function as antioxidants. The genes involved in carotenoid biosynthesis have been studied and provide opportunities for genetic improvement of seaweed. DNA is a basic requirement in molecular analysis. Therefore, a suitable method of DNA extraction from seaweed is needed. The aim of this research was to investigate DNA extraction method from several seaweed species and test the DNA quality through PCR-RAPD. Seaweed samples were collected from Pantai Bumi Perkemahan Taman Nasional Bali Barat and DNA was extracted using Doyle and Doyle’s method with modifications. PCR-RAPD was conducted using primer UBC127 and OPD 11 to test the quality of DNA. Results showed that 3 hours incubation in 60ºC had the best result of DNA extraction. However, the quality of DNA was low, as indicated by inconsistent PCR-RAPD products. Further optimization in DNA extraction is needed to obtain high quality DNA for genetic analysis.
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References
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[2] Fiedor, J., K. Burda. 2014. Potential role of carotenoids as antioxidants in human health and disease. Nutrients. 6(2):466–488doi:10.3390/nu6020466
[3] Ralley, L., E.M.A. Enfissi, N. Misawa, W. Schuch, P.M. Bramley, P.D. Fraser. 2004. Metabolic engineering of ketocarotenoid formation in higher plants. Plant J. 39:477–486
[4] Misawa, N., S. Tomy, K. Kondo, A. Yokohama, S. Kajiwara, T. Saito, T. Ohtani, W. Miki. 1995. Structure and functional analysis of a marine bacterial carotenoid biosynthesis. J Bacteriol. 177(22): 6575-84.
[5] Nishida, Y., K. Adeshi, H. Kasai, Y. Shizuri, K. Shindo, A. Sawabe, S. Komemushi, M. Wataru, N. Misawa. 2005. Elucidation of a carotenoid biosynthesis gene cluster encoding a novel enzyme, 2,2’-β-hydroxylase, from Brevundimonas sp. Strain SD212 and combinational biosynthesis of new and rare xanthophylls. Appl. Environ. Microbiology, 71: 4286-4296
[6] Pereira, J.C., R. Chaves, E. Bastos, A. Leitão, H. Guedes-Pinto. 2011. An efficient method for genomic DNA extraction from different Molluscs species. Int. J. Mol. Sci. 12: 8086-8095; doi:10.3390/ijms12118086
[7] N’Yeurt, ADR.1999. A preliminary illustrated field guide to the common marine algae of the Cook Islands. The University of the South Pacific, Suva, Fiji.
[8] Al-Yamani, F.Y., I. Polikarpov, A. Al-Ghunaim, T. Mikhaylova. 2014. Field guide of marine macroalgae (Chlorophyta, Rhodophyta, Phaeophyceae) of Kuwait. Kuwait Institute for Scientific Research, Safat, Kuwait
[9] Doyle, J.J., J.L. Doyle. 1990. Isolation of plant DNA from fresh tissue. Focus, 12: 13-15
[10] Jain, S.A., F.T. de Jesus, G.M. Marchioro, E.D. de Araújo. 2013. Extraction of DNA from honey and its amplification by PCR for botanical identification. Food Sci. Technol. 33(4): 753-756.
[11] Rogers, S.O., A.J. Benedich. 1985. Extraction of DNA from milligram amounts of fresh herbarium and Mummified plant tissues. Plant Mol. Biol. 5: 69-76
[12] Das, S.S., S. Das (Sur), P. Ghosh. 2013. Optimization of DNA isolation and RAPD-PCR protocol of Acanthus volubilis wall., a rare mangrove plant from Indian Sundarban, for conservation concern. European J. Exp. Biol. 3(6):33-38
[13] Sahu, S.K., M. Thangaraj, K. Kathiresan. 2012. DNA extraction protocol for plants with high levels of secondary metabolites and polysaccharides without using liquid nitrogen and phenol. ISRN Mol. Biol. 2012, Article ID 205049, doi:10.5402/2012/205049
[14] Tan, S.C., B. C. Yiap. 2009. DNA, RNA, and protein extraction: the past and the present. J. Biomed. Biotechnol. 2009, Article ID 574398, doi:10.1155/2009/574398
[15] Shinde, V.M., K. Dhalwal, K.R. Mahadik, K.S. Joshi, B.K. Patwardhan. 2007. RAPD analysis for determination of components in herbal medicine
Evid Based Complement Alternat Med. 4(Suppl 1): 21–23. doi: 10.1093/ecam/nem109.
[16] Skoric, M., B. Šiler, T. Banjanac, J.N. Živkov, S. Dmitrovic, D. Misic, D. Grubisic. 2012. The reproducibility of RAPD profiles: Еffects of PCR components on RAPD analysis of four Centaurium species. Arch. Biol. Sci., Belgrade, 64 (1), 191-199. DOI:10.2298/ABS1201191S191
[17] Bardakci, F. 2001. Random amplified polymorphic
DNA (RAPD) markers. Turk. J. Biol. 25: 185-196
[18] Souza, H.A.V., L.A.C. Muller, R.L. Brandão, M.B. Lovato. 2012. Isolation of high quality and polysaccharide-free DNA from leaves of Dimorphandra mollis (Leguminosae), a tree from the Brazilian Cerrado. Genet. Mol. Res. 11 (1): 756-764
[19] Ramakrishnan, G.S., A.A. Fathima, M. Ramya. 2017. A rapid and efficient DNA extraction method suitable for marine macroalgae. 3 Biotech. 7(6):364. doi:10.1007/s13205-017-0992-2
[20] Wang G, Y. Li, P. Xia, D. Duan. 2005. A simple method for DNA extraction from sporophyte in the brown alga Laminaria japonica. J. Appl. Phycol. 17(1):75–79. doi: 10.1007/s10811-005-5557-9.
[21] Joubert Y., J. Fleurence. DNA isolation protocol for seaweeds. Plant Mol. Biol. Rep. 2005;23:197. doi: 10.1007/BF02772712.
[22] Irvan R. Hengkengbala, G.S. Gerung, S. Wullur. 2018. DNA extraction and amplification of the rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit) gene of red seaweed Gracilaria sp. from Bahoi Waters, North Minahasa Regency. J. Aquatic Sci. Management 6(2): 33-38.
[23] Mohammed, Z.A.A., N.A.H. Al–Bdairi, R.K. Abed. 2018. RAPD marker variability among algae species in Iraq. Biochem. Cell. Arch. 18, Suppl. 1: 953-958.
Published
2020-03-19
How to Cite
BASYAR, Wildan Mujahidul; PHARMAWATI, Made; ASTARINI, Ida Ayu.
Total Genomic DNA Extraction Studies from Seaweeds.
Advances in Tropical Biodiversity and Environmental Sciences, [S.l.], v. 4, n. 1, p. 10-14, mar. 2020.
ISSN 2622-0628.
Available at: <https://ojs.unud.ac.id/index.php/atbes/article/view/58096>. Date accessed: 25 apr. 2024.
doi: https://doi.org/10.24843/ATBES.2020.v04.i01.p03.
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