I have a sample of long chain DNA (~ 100 kb), and it is a mixture of different isoforms (supercoil, relaxed circular, nicked circular, and linear). But I only want relaxed circular from the mixture. Is there a way to separate relaxed circular from the other isoforms? Or can I transform the other isoforms into relaxed circular to get a pure ring sample?
By the way, gel electrophoresis is not working here, since I am trying to get a DNA sample of a dry weight of ~ 1 mg.
Not easy task, a classic way is separation by ultracentrifugation in CsCl. Superhelical DNA can be relaxed by topoisomerases. It could be challenging to separate relax circular and nicked circular DNA, but nicked circular DNA should be sensitive for Exonucleases. Just find the right conditions ... Good luck.
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