Comparison of Real-time PCR fluorescent and non-fluorescent quenchers in standard amplification plots of delta-6 desaturase gene in PANC-1 cell line culture

The present study was undertaken to determine the difference between florescence and non-florescence quenchers and their efficiency in Real-time PCR. PANC-1 cells were cultured in 75cm flasks، 3x106 cells were seeded in 6-well plates and treated with specific signaling drugs، their effect on the expression of delta6 desaturase gene were examined with Real-time PCR in equal conditions، once with florescence and another time with non-florescence quencher. different quenchers absorbances of the fluorescence emission from the reporter، cause different results in Real-time PCR. The amplification plot is more precisely when using non-florescence quencher and its base line is lower. Therefore the signal to noise ratio (S/N) decrease. Also non-florescence quencher with raising the melting temperature cause to decrease in non-specific matching and this led to lower CT ratio. Data showing increased performance of using non-florescence quencher compared to florescence quencher and it can be a better replace for common quencher specially in Allelic discrimination and SNP (single nucleotide polymorphism) studies.