Posted 08 November 2001 - 10:00 PM
Isn't it template contamination? I always thought that the best negative control for PCR was to have a no template tube with you primers, taq, dntp's and buffer. I think that as far as PCR goes, it takes a lot more primer than template to amplify something. With that said, even though my lab uses primers but no template in our negative controls, we still have the same problem you have. Try setting up your reactions under a hood, or in an enclosed, sterile area. Also, try wiping down the inside of your thermocycler and start over with everything fresh. (PCR mix, etc.) If you are sure it is primer contamination, then you might look into getting some type of nucleic acid purification spin columns. Pharmacia is a good place to look. I believe there are some columns that exclude nucleic acids that are smaller than 100bp for example.