One of my favorite things to do with a student the first time they work with DNA plasmid preps is to have them run an agarose gel containing 2 samples: uncut plasmid DNA, and plasmid DNA that has been linearized with an restriction enzyme. I love to have them try and figure out the banding pattern of uncut plasmid DNA (why do you see 2-3 bands?) versus the single band of linearized DNA (and why do all bands convert to 1 band when linearized?).
I like this exercise because understanding the forms they are seeing on the gel requires an understanding of the nature of DNA. In this article I will focus on the four most common species of plasmid DNA observed on a gel and how to recognize them. And in my next article I’ll cover how to increase recovery of the desired supercoiled species.