The leading band (presumably representing supercoiled plasmid DNA) of a 5991bp plasmid containing 3600bp of the lac operon inserted into pBlueScript migrates at a rate approximately equivalent to a 10kb linear fragment. When cut with a restriction enzyme that has one recognition site the plasmid is converted into a 5991bp linear fragment and migrates accordingly. The plasmid has been purified multiple times and consistently yields similar results.
The question was why supercoiled plasmid would migrate much SLOWER than the linear form. I have seen this happen on rare occasions with particular plasmids. In fact, I have two plasmids that have the same insert except for a single base mutation and the supercoiled form of one plasmid migrates SLOWER than the linearized form while the other plasmid behaves normally (supercoiled migrates faster than linear).
The uncut plasmid is assumed as supercoiled form. However in your case when insert is added the plasmid becomes big in size which can have nicks in one strand due to partial degradation or mechanical shearing. The nicked plasmid cannot supercoil and migrates slower than linear plasmid.
Plasmids migrate through gels in three forms, supercoiled, relaxed, and linear. Supercoiled looks the largest, relaxed next and linear the smallest. You are using linear markers and that is why the linear form matches up with your predicted size. It has to do with the way DNA moves through the agarose matrix.
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