Thanks for your suggestions. Do you think primer purification or mycoplasma contamination could be a problem even if the band is of the same size as the product expected in positive control (with DNA)? I am trying to amplify a prokaryotic vector sequence integrated into mouse genome. My primers are from qiagen. One particular set of primers works well with this construct.
I have been contamination problems in my no DNA control of PCR. I have changed all the solutions and have got new primers made. But some how this contaminating band always appears. This happens with a particular DNA clone and not with other clones. Also there is one particular seuence of primers which doesn't give me contamination with this clone. I set up the reactions in a hood. I don't know what to do?