The primers amplify a 432 bp DNA fragment. To specifically amplify T. rubrum and T. mentagrophytes, we aligned the two reference Panobinostat concentration sequences (T. rubrum: Z97993, T. mentagrophytes: Z98000) of the internal transcribed spacer ITS and we chose two sets of specific primers in the site where the sequences were divergent. The selected primers and their PCR product size are shown in Table 2. The primers consisted of the following: Derm primers that amplify all dermatophyte species, TR primer and TM primer that specifically amplify T. rubrum and T. mentagrophytes respectively. Before the MX assays
were set up and to optimise the specificity of the primers, 23 T. rubrum and 35 T. mentagrophytes strains were tested in a species-specific PCR by using separately the TR and TM primers amplifying 214 and 132 bp fragments respectively. After verification of the specificity of each set, we performed a MX PCR using the three primers in the same reaction. Multiplex PCR was performed on DNA extracts from all fungal isolates under the following conditions: the amplification reaction was performed in a total volume of 50 μl; the PCR mixture contained 10 μl of 5× reaction
buffer (GoTaq DNA buffer; Promega, Madison, WI, USA), 0.5 μl of 25 mmol l−1 desoxynucleoside triphosphates containing an equimolar mixture of dATP, dCTP, dGTP and dTTP (Promega), selleck compound 1 μl (30 μmol l−1) of each primer, 1.25 unit of GoTaq DNA polymerase (Promega) and 50 ng of template DNA. Samples were amplified through 30 cycles in a thermocycler (Thermolyne Amplitron II Series 1091, Barnstead Thermolyne Corporation, Dubuque, IA, USA) as follows: initial denaturation for 5 min at 95 °C, denaturation for 30 s at 94 °C, annealing for 30 s at 60 °C and extension for 30 s at 72 °C. This was followed by a final extension step for 10 min Docetaxel mw at 72 °C.
PCR products were separated on 2% agarose gel, stained with ethidium bromide and visualised under an UV illumination. Appropriate positive and negative controls were included in every amplification. Analytical sensitivity was determined using serial dilutions (starting from 5 pg up to 50 pg per reaction) of purified DNA extracted from the two reference targets: T. rubrum CBS 494.62 and T. interdigitale CBS 165.66. DNA was extracted from pure cultures as described by Liu et al. . Common dermatophytes, reference strains, non-dermatophytic moulds, yeast and human DNA were used to determine the specificity of the MX PCR (Table 1). Data from mycological test and MX PCR were compared using analysis of chi-squared test as appropriate. The level of statistical significance was set at P < 0.05. Figure 1 shows PCR results with Derm, TR and TM primers by using serial dilution of extracted DNA; starting from 5 pg up to 50 pg per reaction. The lowest concentration of DNA that gave a positive MX PCR result for all the investigated dermatophyte species was 50 pg in a PCR volume of 50 μl.