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Why does a plasmid that has never been cut give two or three bands on an agarose gel?

When plasmid DNA is extracted from bacterial cells, we get what we consider a purified product, but the plasmid will usually be present in three distinct topological forms. As described on the following pages, these three forms, known as Supercoiled, Relaxed Circle and Full-length Linear, are all the same size, but have different shapes.

The confusing thing about them is the way we think of our gels. We usually think of them as separating DNA according to size, but this is only true if all the molecules in the sample have the same shape. The SHAPE of the molecule will, however, affect the rate of migration in a gel. As shown here, it is possible to see all three forms of the same-sized molecule in the same lane of a gel. It is actually more common for the two upper bands to run together as one.

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