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.
Copyright University of Maryland, 2007
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