Endocervical swab samples were obtained from the patients. Each swab was placed in a sample collection vial containing the buffer (PBS). Several methods are available for DNA extraction. In the present study, we used the boiling method. We selected one pair of oligonucleotide primers (Cinnagen, Iran) specific for a region of the C. trachomatis gene (accession No. AB695165.1), coding for the major outer membrane protein (MOMP). The sequences from 5' to 3' of these oligonucleotide primers are as follows:
A master mixture of these reagents was made for the samples along with the positive and negative controls. The final reaction mixture of 50 µL for each sample contained 0.5 µM of each primer; 100 µM of each of dATP, dCTP, dGTP and dTTP; 50 mM KCl; 10 mM Tris-HCl, pH 8.3; 1.5 mM MgCl
2, 1.25 units of Taq DNA polymerase enzyme, and 9 µL of the sample DNA. All the PCR reagents were purchased from the SinaClon company, Iran. Each microfuge tube containing the PCR mixture of 50 µL was mixed and subjected to 40 cycles of amplification. Each cycle composed of sequential incubations at 94°C for 1 minute for DNA denaturation, 52°C for 1 minute for annealing the primer to the templates, and 72°C for 30 seconds for DNA chain extension. At the end of the 40 cycles, the samples were kept for another 7 minutes at 72°C for completion of the extension of a DNA chain. The PCR product samples were immediately frozen for further analysis. The PCR products were visualized by agarose gel electrophoresis. A 10-µL post-PCR mixture was subjected to electrophoresis on 2% agarose gel (SinaClone, Iran) in the presence of ethidium bromide (Sigma, Germany). A DNA ladder (SinaClone, Iran) was also run simultaneously to confirm the size of the amplified product (103 bp) (
Figure 1). The DNAs were extracted from the bands on the gel using a gel extraction kit (Qiagen, GmbH, Germany) and then sequenced by Macrogen Inc, Seoul, Korea.