Question of q-pcr primer design
Posted 09 August 2010 - 07:26 AM
I am new to qPCR. I used Primerquest from IDTDNA to design the primers for qPCR. The Tm parameters were set as 60-64C, 62C optimal. However when I check the primers IDT recommended, Tm is around 55C (by manually adding up G/C=3 A/T=2). A regular PCR was performed with annealing T as 60, only 3 of 10 got bands (right ones at 100-150 bp and unspecific ones at 400 bp and top).
Double checked with IDT website, it claimed that the latest concept of calculating Tm is to integrate consideration of salts in reaction buffer thus when using their software to design q-pcr primers Tm will be calculated based on standard qPCR parameters (50 mM K, 3 mM Mg, 0.8 mM dNTPs). Does this mean a primer with Tm of 55C in 50 mM NaCl will work as Tm of 60C in a q-PCR? I am going to use Power SYBR® Green PCR Master Mix from AB which the salts concentration is not released. Getting quit confusd now.
Does anybody get this problem before or clear out the mystery. Any thoughts are appreciated.
Posted 10 August 2010 - 12:35 AM
Posted 10 August 2010 - 07:20 AM