I have encountered an unusual problem with my cloning and wondering if anyone else has experienced this and what the problem might be.
I have performed a simple cloning using digest/ligation etc. All steps appeared to work fine and I got plenty of colonies from my E.coli transformation. I screened colonies by colony PCR and found some candidates with the expected size product.
However when I went to confirm these candidates by restriction digest I found multiple bands on my agarose gel. At first I presumed a mistake (wrong enzymes perhaps) so I repeated the miniprep and this time before doing the digest I ran a sample of just DNA on a gel.
This also showed multiple DNA bands per sample, so my question is how is this possible when I only transformed 1 DNA ligation product into my competent cells? Could it be some sort of contamination? But it was in every sample (although not the same sizes of band patterns in every one).
Any thoughts/advice/solutions greatly appreciated.