PCR contamination problem - (Mar/07/2012 )

I have been genotyping mice for the last 3 months. My PCRs from genomic DNA extracted from the mice's ears were fine, giving the right bands. Two weeks ago things started to get pear-shaped: contamiantion. I changed all the solutions, one by one, to pin-point which one of the reagents was the contamiantion culprit. Eventually I did PCR with water as template and there was no product so I assumed the PCR was now cleaned!. Whe I introduced the sample DNA in the PCR, still I get weak bands where I shouldn't (eventhough the water control is clean). I have no idea of what it's going on. This is very annoying since I need to sort out the genotype for the mice. Anyone has any suggestions about what it might be happening?

Thanks in advance.
Chivite

Sounds like your tube of mouse ear DNA is contaminated. Can you take another sample? toe, tail etc.? If you keep getting the same banding pattern, cut out the bands and sequence them so you know what they are.

It might also be the primers. I cannot exactly explain why, but sometimes "something" happens to the primers that start amplifying different sequences besides the one you'r interested in.
It bothers me having to use these terms like "something".. but in fact the same thing happened to me... I just got new primers and everything started working perfectly...