| | Re: Amplification in negative control
Try to prepared the negative control before you even handle any sample DNA, seal the tube after that and do not open it until gel electrophoresis (or whatever you do after the thermal cycling is over).
ALWAYS clean the PCR work place with 70% etoH or diluted bleach and try to avoid air currents while handling opened reagent or sample tubes. A hood with UV light is useful: You can irradiate the surface for 20 min before working. You can even irradiate some of the PCR reagents such as water, PCR buffer and MgCl2 (other reagents are UV sensitive), as well as any equipment you use like pipettes, tip boxes and such.
Another tip is to try not to touch the surfaces of the tubes with the pipettes (just with the pipette tip) as this is a potencial cause of reagent contamination.
Hope this helps.