MathBench > Visualization

Chopping up plasmids

dna circleOther weirdnesses

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:

  1. "nicked" dnaIf 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).
  2. linear dnaIf 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.
  3. supercoiled dnaIf 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.