Genetics--Circular DNA molecules?

Question

Circular DNA molecules of the same size migrate at different rates in electrophoretic gels depending on whether they are supercoiled or relaxed circles. Why?
Also is the speed of migration affected in both? Is it greater in supercoiled or relaxed?

Thank you!

both are good answers I dont know which to choose...so I'll let it go into voting

Answer 1

Supercoiling makes the DNA compact into a smaller chunk. Therefore, compared to a relaxed circle of DNA, supercoiled DNA should migrate farther.

As for migration speed, I'm not sure. I think that'd be determined by the dispersion of charges on the DNA strand. If more charges are concentrated outwardly, shouldn't that attract to the electrode more and faster?

Answer 2

When you're dealing with gels, everything is about how quickly the DNA can physically move through the matrix, nothing to do with the charge.

Two same-sized DNA sequences in a plasmid will supercoil to the same size, as supercoiling has nothing to do with the base sequence.

If you look at a gel of a plasmid prep, you'll often see three bands. They are in order of decreasing apparent size, nicked (relaxed), supercoiled, linear (full-through cut). Imagine a circle of DNA - unless it's super-coiled, it's flexible but not very. Imagine trying to push a tennis ball through a pool of jello, compared with a somewhat-bendy hula hoop (okay, that's an exaggeration, but you get the idea?). The full-through cut plasmid travels the fastest of all, as it can slither through the matrix end-first.

Incidentally, if you add an intercalator (ie ethidium bromide, a stain normally used in gels) to the gel prior to running it, as many labs (mine included) do, you'll see the distance between the nicked and supercoiled bands decrease. The intercalator (something that gets in between the bases) undoes the supercoiling, making the 'supercoiled' pasmid more and more like the nicked plasmid.