Pengaruh Konsentrasi Polivinilpirolidon (PVP) terhadap Kualitas dan Kuantitas Isolasi DNA EukCC

Authors

  • Chika Shafa Maura Universitas Negeri Jakarta
  • Imam Safir Alwan Nurza Institut Pertanian Bogor

Keywords:

Eukariot, Isolasi DNA, Polivinilpirolidon, Prokariot

Abstract

Isolasi DNA merupakan tahap penting dalam aplikasi biologi molekuler, termasuk diagnostik dan penelitian genetik. Polivinilpirolidon (PVP) diketahui sebagai agen penstabil dalam berbagai proses kimia dan biologi. Tujuan penelitian ini dilakukan untuk mengevaluasi pengaruh konsentrasi PVP 1% dan 2% terhadap kualitas dan kuantitas isolasi DNA sel eukariot dan prokariot. Metode penelitian yang digunakan adalah CTAB dengan konsentrasi PVP (1%, dan 2%) diuji untuk menentukan kondisi optimal. Proses isolasi DNA melibatkan lisis sel, pemurnian, dan pengendapan DNA. Kualitas DNA diamati dengan elektroforesis dan spektrofotometri untuk mengukur konsentrasi dan kemurnian DNA sebagai kuantitas DNA. Eukariot yang digunakan berupa tanaman Ananas comosus var. Toboali dan cendawan Trichoderma sp. Sedangkan prokariot berupa bakteri Escherichia coli (E. coli). Hasil penelitian menunjukkan penggunaan PVP meningkatkan kuantitas DNA yang diisolasi tanpa mengurangi kualitasnya. PVP 2% memberikan hasil dengan kemunculan pita pada isolasi DNA eukariot. PVP 1% memberikan kualitas yang sangat baik pada prokariot dengan kemunculan pita tegas. Oleh karena itu, penggunaan konsentrasi PVP yang tepat dapat meingkatkan efisiensi dan efektivitas isolasi DNA dari sel eukariot dan prokariot.

References

Aamir, S., Sutar, S., Singh, S. K., & Baghela, A. (2015). A rapid and efficient method of fungal genomic DNA extraction, suitable for PCR based molecular methods. Plant Pathology & Quarantine, 5(2), 74–81. https://doi.org/10.5943/ppq/5/2/6

Abdel-Latif, A., & Osman, G. (2017). Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods, 13, 1. https://doi.org/10.1186/s13007-016-0152-4

Almakarem, A. A. S., Heilman, K. L., Conger, H. L., Shtarkman, Y. M., & Rogers, S. O. (2012). Extraction of DNA from plant and fungus tissues in situ. BMC Research Notes, 5, 266. https://doi.org/10.1186/1756-0500-5-266

Al-Samarrai, T. H., & Schmid, J. (2000). A simple method for extraction of fungal genomic DNA. Letters in Applied Microbiology, 30(1), 53–56. https://doi.org/10.1046/j.1472-765X.2000.00664.x

Asad, N., Cregg, S., Shakya, S., Stegman, S., & Timmons, L. (2023). Sustainable and cost-effective gel documentation. Methods and Protocols, 6(2), 21. https://doi.org/10.3390/mps6020021

Badal, S., & Delgoda, R. (2017). Pharmacognosy: Fundamentals, applications and strategies. Elsevier.

Bendich, A. J. (2007). The size and form of chromosomes are constant in the nucleus, but highly variable in bacteria, mitochondria and chloroplasts. BioEssays, 29(5), 474–483. https://doi.org/10.1002/bies.20576

Boldura, O. M., Balta, C., & Awwad, N. S. (2020). Biochemical analysis tools: Methods for bio-molecules studies. IntechOpen.

Branton, D., & Deamer, D. (2019). Nanopore sequencing: An introduction. World Scientific.

Carr, E. (2022). CTAB DNA extraction protocol for fungi. Protocols.

Carter-House, D., Stajich, J. E., U’Ren, J., & Arnold, A. E. (2020). Fungal CTAB DNA extraction. Protocols.

Conlon, B. H., Schmidt, S., Poulsen, M., & Shik, J. Z. (2022). Orthogonal protocols for DNA extraction from filamentous fungi. STAR Protocols, 3(1), 101126. https://doi.org/10.1016/j.xpro.2022.101126

Francioli, D., Lentendu, G., Lewin, S., & Kolb, S. (2021). DNA metabarcoding for the characterization of terrestrial microbiota: Pitfalls and solutions. Microorganisms, 9(2), 361. https://doi.org/10.3390/microorganisms9020361

Fredricks, D. N., Smith, C., & Meier, A. (2005). Comparison of six DNA extraction methods for recovery of fungal DNA as assessed by quantitative PCR. Journal of Clinical Microbiology, 43(10), 5122–5128. https://doi.org/10.1128/JCM.43.10.5122-5128.2005

Galliano, I., Daprà, V., Zaniol, E., Alliaudi, C., Graziano, E., Montanari, P., Calvi, C., & Bergallo, M. (2021). Comparison of methods for isolating fungal DNA. Practical Laboratory Medicine, 25, e00221. https://doi.org/10.1016/j.plabm.2021.e00221

Gautam, A. (2022). DNA and RNA isolation techniques for non-experts. Springer Nature.

Goldschmidt, P., Degorge, S., Merabet, L., & Chaumeil, C. (2014). Enzymatic treatment of specimens before DNA extraction directly influences molecular detection of infectious agents. PLOS ONE, 9(6), e94886. https://doi.org/10.1371/journal.pone.0094886

Greco, M., Sáez, C. A., Brown, M. T., & Bitonti, M. B. (2014). A simple and effective method for high-quality co-extraction of genomic DNA and total RNA from low biomass Ectocarpus siliculosus, the model brown alga. PLOS ONE, 9(5), e96470. https://doi.org/10.1371/journal.pone.0096470

Haque, S., Ashraf, N., Awal, A., Sarker, R. H., Begum, S., & Khan, H. (2004). Method for quality DNA isolation from different parts of jute plant: Corchorus capsularis L. and C. olitorius L. Plant Tissue Culture, 14(2), 143–148.

Healey, A., Furtado, A., Cooper, T., & Henry, R. J. (2014). Protocol: A simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods, 10, 21. https://doi.org/10.1186/1746-4811-10-21

Intarapanich, A., Kaewkamnerd, S., Shaw, P. J., Ukosakit, K., & Tragoonrung, S. (2015). Automatic DNA diagnosis for 1D gel electrophoresis images using bio-image processing technique. BMC Genomics, 16(Suppl. 12), S15. https://doi.org/10.1186/1471-2164-16-S12-S15

Kim, J. S., Seo, S. G., Jun, B. K., Kim, J. W., & Kim, S. H. (2010). Simple and reliable DNA extraction method for the dark pigmented fungus, Cercospora sojina. The Plant Pathology Journal, 26(3), 289–292. https://doi.org/10.5423/PPJ.2010.26.3.289

Kumar, M., & Mugunthan, M. (2018). Evaluation of three DNA extraction methods from fungal cultures. Medical Journal Armed Forces India, 74(4), 333–336. https://doi.org/10.1016/j.mjafi.2017.07.009

Lee, B. J., Kim, S., Lee, J. W., Lee, H. M., & Eo, S. H. (2021). Technical note: Polyvinylpyrrolidone (PVP) and proteinase-K improve the efficiency of DNA extraction from Japanese larch wood and PCR success rate. Forensic Science International, 328, 111005. https://doi.org/10.1016/j.forsciint.2021.111005

Lee, P. Y., Costumbrado, J., Hsu, C. Y., & Kim, Y. H. (2012). Agarose gel electrophoresis for the separation of DNA fragments. Journal of Visualized Experiments, 62, e3923. https://doi.org/10.3791/3923

Leuko, S., Goh, F., Ibáñez-Peral, R., Burns, B. P., Walter, M. R., & Neilan, B. A. (2008). Lysis efficiency of standard DNA extraction methods for Halococcus spp. in an organic rich environment. Extremophiles, 12, 301–308. https://doi.org/10.1007/s00792-007-0124-8

Lever, M. A., Torti, A., Eickenbusch, P., Michaud, A. B., Šantl-Temkiv, T., & Jørgensen, B. B. (2015). A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types. Frontiers in Microbiology, 6, 476. https://doi.org/10.3389/fmicb.2015.00476

Magdeldin, S. (2012). Gel electrophoresis: Principles and basics. IntechOpen.

Michiels, A., Van den Ende, W., Tucker, M., Van Riet, L., & Van Laere, A. (2003). Extraction of high-quality genomic DNA from latex-containing plants. Analytical Biochemistry, 315(1), 85–89. https://doi.org/10.1016/S0003-2697(02)00665-6

Nilsson, R. H., Tedersoo, L., Ryberg, M., Kristiansson, E., Hartmann, M., Unterseher, M., Porter, T. M., Bengtsson-Palme, J., Walker, D. M., de Sousa, F., Gamper, H. A., Larsson, E., Larsson, K. H., Kõljalg, U., Edgar, R. C., & Abarenkov, K. A. (2015). Comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts. Microbes and Environments, 30(2), 145–150. https://doi.org/10.1264/jsme2.ME14121

Pandey, A., & Teixeira, A. J. C. (2017). Current developments in biotechnology and bioengineering: Foundations of biotechnology and bioengineering. Elsevier.

Patrinos, G. P. (2017). Molecular diagnostics. Elsevier.

Pilo, P., Tiley, A. M. M., Lawless, C., Karki, S. J., Burke, J., & Feechan, A. (2022). A rapid fungal DNA extraction method suitable for PCR screening fungal mutants, infected plant tissue and spore trap samples. Physiological and Molecular Plant Pathology, 117, 101758. https://doi.org/10.1016/j.pmpp.2021.101758

Rantakokko-Jalava, K., & Jalava, J. (2002). Optimal DNA isolation method for detection of bacteria in clinical specimens by broad-range PCR. Journal of Clinical Microbiology, 40(11), 4211–4217. https://doi.org/10.1128/JCM.40.11.4211-4217.2002

Riffiani, R., Wada, T., Shimomura, N., Yamaguchi, T., & Aimi, T. (2021). An optimized method for high-quality DNA extraction medicinal fungi Mycoleptodonoides aitchisonii for whole genome sequencing. IOP Conference Series: Earth and Environmental Science, 948, 012032. https://doi.org/10.1088/1755-1315/948/1/012032

Sambrook, J., & Russell, D. W. (2001). Molecular cloning (3rd ed.). Cold Spring Harbor Laboratory Press.

Sophian, A., & Syukur, A. (2021). Short communication: Analysis of purity and concentration of isolated DNA in making raw DNA of rat species. ERUDITIO, 1(2), 1–5. https://doi.org/10.54384/eruditio.v1i2.75

Umesha, S., Manukumar, H. M., & Raghava, S. (2016). A rapid method for isolation of genomic DNA from food-borne fungal pathogens. 3 Biotech, 6(2), 123. https://doi.org/10.1007/s13205-016-0436-4

Yee, W., Kumar, J. N., & Muthusamy, P. D. (2018). Inclusion of 2-mercaptoethanol in lysis buffer could interfere with isolation of high molecular weight DNA from freshwater microalgae. Indian Journal of Microbiology, 58(1), 109–113. https://doi.org/10.1007/s12088-017-0698-5

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Published

2024-12-31