Question

Explain why a circular plasmid runs differently than a linearized plasmid on a gel.

Answer 1

Plasmid DNA exists in three different conformations : supercoiled (covalent closed circular), open-circular, and linear.

In supercoiled conformation, the DNA fragments become smaller in size and hence experience less friction on a gel, results in faster migration than other conformations.

In case of linearized plasmid, both the strands of supercoiled DNA fragment broken due to nick or cut, the circular double helix becomes linear. Because of this conformation it migrates according to its size.

When one of the double strands of circular DNA fragment is broken and results in open circular conformation. Size of DNA molecule increses in this conformation and hence it experiences more friction on  gel. Due to increase in size, the migration of open-circular DNA is slower than other conformations.

The increasing order of migrating different conformation of plasmid DNA are given as:

supercoiled>linear>open-circular.

The variation in the size of different conformation is the main reason why circular plasmid runs diffrently than a linearized plasmid on a gel.