Primer dimer problem in MSP - (Aug/26/2008 )

With many help from here, I finally got specific MSP bands for several primer sets.

However, for one primer set, there still is a band below 100 bp, which I guess is a primer dimer.
(I ordered the primer that had been used in two papers)

There is also the specific right-sized band of ~200 bp. The purpose of this experiments is to quantify the methylation of the gene by MSP.

1. Can I just compare the amount of PCR band at the specific size even if there exists a primer dimer band? or should I find the PCR condition that brings no primer dimer band?

2. Then, how can I get rid of the primer dimer band? I am using hotstart Taq and primers at concentration of 200nM, and what do you recommend I should try next?

If you quantify methylation, you do need to concern the dimer issue, since primer dimers will affect the efficiency of PCR.

You can try to lower down the concentration of primers first, as well as use DMSO. If you still can not fix the problem, email your primer sequence and target gene, I would like to help you.