The parameters primer "self-annealing" in Primer 3 should - if possible - be set to a max. of 3 or even less; in this way primer dimer formation may be minimized. In addition, I would recommend using a hot-start Taq in your PCR reaction.
First Analyse your primer self- and hetero-dimer TM and Delta G. Make sure TM of dimer is less than annealing TM. Delta G should be less than 7. If you have no more choice and use these primers. increase template DNA. Using hot start enzyme might be helpful
Most important variable is "Max 3' Self Complementarity:" set as low as possible. However this may not guarantee complete absence of 3' self /cross dimers. Check the designed primers with a software like Oligoanalyser and confirm that there is no 3' extensible primer-dimers.
First. We do an additonal check with M-fold. If M-fold points to self complementarity we move primers one positon to the right, or the left and check once more. We use Allele-ID of Premier Biosoft. M-fold is included in this program. Our experience is that primers selected with primer3 are sometimes disapproved in Allel-ID.
Even wehn you check all these parameters dimers may appear when your reaction conditions are imperfect. We have good experiences to analyse the qPCR with a temperature gradient. You might have the wrong annealing temperature. We also observed a subtile balance between matrix, inital target mount and primer concentration. So you can loer primer concnetration. The Cq does noet differ at lower primer concentrations. Only a lower plateau is reached.
I presume that temperature gradient PCR is the same as I suggested as "q PCR with a te,erature gradient"
If you have already designed your primers, then you don't have the option of changing delta G. so I will recommend you to increase the anneling temp just 1 degree. I have good experience of doing this.
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