DNA extraction method of pathogenic fungi and the optimization of simple sequence repeat PCR system

Yanqiu YANG; Li WANG; Dan HE; Koji YOKOYAMA

ABSTRACT

BACKGROUND:

Extraction of fungal DNA plays an important role in fungal genetic engineering and molecular biology research.The result of experiment is affected seriously by the efficiency of extracting DNA especially the quality of DNA.

OBJECTIVE:

To develop a method for extracting genomic DNA of pathogenic fungi and discuss the optimal combination of components in simple sequence repeat PCR (SSR-PCR) system. DESIGN, TIME AND

SETTING:

A comparative analysis of DNA extraction methods and an orthogonal experiment were conducted in the Mycology Research Lab of Department of Pathogenobiology in Norman Bethune College of Medicine, Jilin University from July 2004 to December 2006.MATERIALS Clinical specimens were inoculated on Potato dextrose agar, Potato dextrose broth and Yeast extract peptone dextrose and cultivated under the temperature of 28 ℃ for 3-7 days, after which suspectable colonies were selected to be isolated and purified.

METHODS:

Three kinds of methods of extracting DNA(beading-salt fractionation method, CTAB method and Gene TLE~(TM) extraction method ) were compared in terms of their effects on DNA quality; Experiment was performed with orthogonal design to four factors (Taq DNA polymerase, template DNA, dNTP, primers) in three levels on the basis of L9 (3~4) orthogonal table, The appropriate annealing temperature and cycles were determined through PCR.MAIN OUTCOME

MEASURES:

The optimal reaction system determined according to the polymorphism and specificity of amplification of banding pattern.

RESULTS:

The objective fragments were all amplified by Gene TLE~(TM) extraction method, and the banding patterns obtained were clearer and brighter compared with the other two methods. The result of orthogonal experiment on SSR-PCR system showed that,according to the value of R, the significance of factors followed by ascending were template DNA (2.67), Taq DNA polymerase (2.00), dNTP (0.67) and primers (0.33). According to the value of ki, the optimal level of each factor combination was 30 mg/L template DNA, 1U Taq DNA polymerase, 150 μmol/L dNTP, 0.5 μmol/L primer. However, because primers were nonsignificant factors, which was presented by their small R value, we took A level of primer as 0.25 μmol/L. The best reaction condition was 55 ℃ annealing temperature and 35 cycles.

CONCLUSION:

The Gene TLE~(TM) method shows higher efficiency of extracting DNA and its operation is fast and simplel According to the results of orthogonat experiment, the optimal SSR-PCR system was 30 mg/L template DNA, 1U Taq DNA polymerase, 150 μmol/L dNTP and 0.25 μmol/L primer. The best reaction condition was 55℃ annealing temperature and 35 cycles.