There are really strange bands in agarose gel electrophoresis of PCR product. I tried to get approx. 400 bp large amplicon from 16S rRNA gene of bacterial gDNA, which I did, but there are also bands larger than 10 kb and negative control is positive (the same length as target product). I have tried several Mg2+ concentrations, gradient PCR, new reagents, working in UV laminar flow cabinet but results are the same. I put in agarose gel the same (not shown in picture) quantity of gDNA that I used for PCR reaction (50 ng). Nothing appeared there.
Ok, I could extract the product from gel, but there might be a huge loss + it won't remove something that is in negative control.
The problem is the same when I'm using primers for 1.4kbp. Maybe I should purify template DNA?
I attached a photo of the agarose gel.
Any suggestions? Thank you!
Edited by krisinthelab, 19 January 2012 - 01:31 PM.