I've been attempting to isolate 16S rDNA from bacteria grown on contact lenses for several months now but always seem to get some sort of inhibitor when I run PCR. My positive control works great (just E. coli DNA) but when 1 uL sample is added to the control I get no amplification. I have very little sample left but have a good concentration for approximately 150 ng/uL based on my nanodrop-1000. I've tried dilutions down to 1:1000 for the samples and still get inhibition. We've also used several DNA cleaning columns and alcohol precipitations to try and get it out but no luck. Any ideas?
P.S. my 260/280 ratios are 1.84 and 260/230 is 1.32
Thanks for your help!