Protocol Online logo
Top : Forum Archives: : Real-Time PCR

RT PCR Primer dimer tissue dependent SYBR - (Jul/17/2007 )


I have some primers that work perfectly in kidney tissue but the same primers produce large primer dimers when I use them in the brain.

I know the brain RNA is good quality as other primers from the brain sample are fine - using a protocol to take into account lipid rich tissue.

Am I right in thinking if the target cDNA sequence is very low then primer dimers are more likely. Is it a case of reducing the primer concentration in the brain tissue to reflect the low amount of target template ?

Is DMSO the answer or an extra step in the protocol to remove the p/dbefore capture ?

Currently at 100nm for F/R primers.

Many thanks in advance.


I think you are on the correct trace... if the amount of your mRNA of Interest is very low in the brain, than PDs are much more likely to form. I would try lowering the primer concentration or maybe perform the first five cycles with an elevated Tm.