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Dilin Rahayu Nataningtyas
Faculty of Mathematics and Natural Science, Universitas Gadjah Mada, Yogyakarta 55281
Chemical Engineering, Chemistry & Bioengineering Chemistry

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COMPARATIVE EVALUATION OF CONVENTIONAL VERSUS RAPID METHODS FOR AMPLIFIABLE GENOMIC DNA ISOLATION OF CULTURED Azospirillum sp. JG3 Stalis Norma Ethica; Dilin Rahayu Nataningtyas; Puji Lestari; Istini Istini; Endang Semiarti; Jaka Widada; Tri Joko Raharjo
Indonesian Journal of Chemistry Vol 13, No 3 (2013)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (397.032 KB) | DOI: 10.22146/ijc.21284

Abstract

As an initial attempt to reveal genetic information of Azospirillum sp. JG3 strain, which is still absence despite of the strains' ability in producing valued enzymes, two groups of conventional methods: lysis-enzyme and column-kit; and two rapid methods: thermal disruption and intact colony were evaluated. The aim is to determine the most practical method for obtaining high-grade PCR product using degenerate primers as part of routine-basis protocols for studying the molecular genetics of the Azospirillal bacteria. The evaluation includes the assessment of electrophoresis gel visualization, pellet appearance, preparation time, and PCR result of extracted genomic DNA from each method. Our results confirmed that the conventional methods were more superior to the rapid methods in generating genomic DNA isolates visible on electrophoresis gel. However, modification made in the previously developed DNA isolation protocol giving the simplest and most rapid method of all methods used in this study for extracting PCR-amplifiable DNA of Azospirillum sp. JG3. Intact bacterial cells (intact colony) loaded on electrophoresis gel could present genomic DNA band, but could not be completely amplified by PCR without thermal treatment. It can also be inferred from our result that the 3 to 5-min heating in dH2O step is critical for the pre-treatment of colony PCR of Azospirillal cells.
Co-Authors Endang Semiarti Istini Istini Jaka Widada Puji Lestari Stalis Norma Ethica Tri Joko Raharjo