Problems with several unspecific bands after PCR - (Oct/12/2007 )

I have come across a very interesting bacterial isolate and I decided to sequence its 16 S rRNA gene. I have therefore extracted some genomic DNA and used this as template in a PCR designed to amplify the whole genome. I was expecting one band, but got three bands: at 40 bp, 700 bp and 1500 bp.

What I don't understand is why there are several PCR products and what I should do to solve this problem and obtain the sequence information that I am interested in?

Try raising your annealing temperature. What primers are you using? You might want to look at these articles:
http://openwetware.org/wiki/Bacterial_species_identification

Thanks! I've solved the problem by designing new primers.