Hi Gayatri,

Is the band you observe in your negative control of smaller size than your samples (generally at the bottom of the gel)? Then it most likely indicates primer dimer formation and you might want to design new primers. Most likely, however, you are observing a band of the same size as your positive control and/or your samples, right? If that's the case, you are experiencing some kind of template contamination in one of your reagents/solutions. It could take a while to identify which one (you would have to set up negative controls excluding one of the old reagents at a time), so my suggestion is to repeat your experiment using all fresh reagents. Also clean your pipettes well, as they can also be a source of contamination, and use filter tips, if possible.

If you could provide more information on the setup of your experiment (starting material, nature of negative control etc), maybe we can pinpoint better the cause of your positive negative control.

Regards,

Elena