I have been using the Euromedex BACTH system to test for protein interaction. After repeatedly selecting for my “prey” plasmid, I was unsuccessful dropping the “bait” plasmid. I decided to design primers for the binding site on the bait plasmid and PCR it for downstream sequencing. After creating a plasmid prep and doing PCR, the gel showed heavy bands of my anticipated DNA size, but also showed well defined bands that I could not identify. I ensured that the primers I designed would only bind to my “prey” vector, so I am unsure how I am getting different PCR bands. Could there be some odd genetic event happening through PCR that is causing the plasmids to recombine or something of the sort, therefore potentially making new primer binding sites? Thanks.