Design of a new method of ARMS PCR for detection of MMP-9 promoter -1562 C/T polymorphism

Type IV collagens is one of the most important genes which due to its function in collagen digestion can be affective in separation of the cells from the basal lamina and the metastasis of them so this gene is known as a tumor marker of several cancers. Existence of a single nucleotide polymorphism -1562 C/T at this gene’s promoter case leads to over expression of this gene in transcription level by decreasing inhibitor protein bonding on T alleles. The aim of the present study was to investigate a new method for the person’s genotype on this polymorphism without the use of PCR_RFLP. Using EPD genome database, the sequences of the intended region were received and by using PRIMER1 software 4 primers were designed for the area. With multiple PCR reaction, two pairs of the best primers were selected and the ARMS PCR was optimized for them. The PCR genotyping results were approved by direct Sequencing. With the use of the newly designed primers, the ARMS PCR product with 205 nucleotide size showed C allele and the PCR products with 253 nucleotide sizes showed the T allele. With the use of this technique, we can determine the person’s genotype with an ARMS PCR without the use of RFLP and with a higher speed and accuracy.