Sec. structure in primers - (Jun/08/2015 )

Hi,

I seem to have very weak to weak sec. structure in some of the primers i designed. Does/Will it affect my qPCR reaction in any way? Secondly, is there any way of getting rid of the sec. structures without re-designing the primers?

Thanks :)

Maybe is the best answer you will get with regard to secondary structure affecting your PCR.

You can use DMSO or betaine in conventional PCR to inhibit secondary structure fomation, but I don't know if this addition will affect qPCR.