I'm working with a pET vector that should be 6.1 kb with my insert. Initially, I had some trouble with our cloning strains (XL1 blues) and was running out of plasmid, so ended up transforming BL21 DE3 pLysS cells. I miniprepped from those but am now seeing something strange. When analysed on a 1% agarose gel, I get 6 bands (way more than I'd expect from supercoiling) and, when linearised, shows a size of between 10-12kb.
Is is possible that the plasmid was somehow recombined by the BL21 cells? Why is it double the size it should be?