Occasionally you may see other artefacts in the gel electrophoresis process — extra bands that don’t correspond to any of the fragments. Here’s how that can happen:
- If only one strand of the double helix gets cut, we say the circle has been “nicked“. Then it loses its ability to coil and becomes limp. This big, floppy mess of DNA has a hard time moving through the gel, so it appears to be a very large fragment (even larger than the plasmid itself).
- If the circle only gets cut at one restriction site (rather than at all restriction sites), the result is a linear piece of DNA that has the same length as the total plasmid. This big strand of DNA has to be oriented pointy-side first to get through the gel, so naturally it doesn’t get very far.
- If a plasmid supercoils, it compacts itself and can move very quickly through the gel. Thus, even though it has not been cut, it appears to be a very small fragment.