You need to distinguish primer-dimers (typically 50-80 bp bands) from primer stock contamination, which will yield large fragments. I'm guessing your primer stocks have contamination. There's nothing to do for that except to reorder the primers and aliquot them on delivery.

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Hey

I also thought those primer-dimers/what ever the bands I am seeing are because of the some contamination in the primers.So I have diluted newly ordered set of primers with the un-contaminated water.But still those bands showed up.I think there is some thing else going on other than primer contamination.

Thank you,

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Hey guys,

I was able to amplify IS6110 (123bp) fragment from M.BCG. When my PCR was good, my negative control(with no DNA) used to show up some primer-dimer band far from the 100bp DNA ladder band. Now the problem is sometimes my Negative control is also showing up the band same as my BCG IS6110 band that is 123bp.I am not seeing this negative control band with any of other primers. Therefore I thought this problem could be because of the primers. So I freshly diluted the primers from my stock and tried the PCR and still it showed up that 123bp band. I also tried the same PCR with another set of same primers that used to work very well before but still that 123bp band showed up in my negative control. I don’t think my problem is with the reagents because they are working very well with the remaining primers. Please advise me something what I could try on this issue.

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