I would like to ask if someone has any experience or Ref on the stability comparison of the above said plasmid DNA (linearized and circular plasmid DNA, stored at same storage conditions). What methods would you suggest to perform the comparison test ?
Thank you very much ~
Circular plasmids are more stable, as there are no ends from which degradation can easily occur. An easy test would be running a gel after storing both for a considerable time (short to medium term storage should gardly make a difference, DNA is very stable, after all). You should see more of a smear in the linearized sample, as it will consist of more differently-sized fragments.
You don't mention anything about how the DNA was isolated: If there are protein contaminants, these are just as likely to be exonucleases as endonucleases and only in the former case would the linear DNA be less "stable" (although the effect would be very difficult to assess using gels as the size change would be miniscule unless there was a massive contamination). But that raises the question of what you mean by "stability"??
I would argue that if your assessment of stability is based on agarose gels, then circular will be less stable than linear. Circular is supercoiled, and just one single strand break will relax this and the DNA will migrate more slowly in the gel. Such events in linear DNA will not be detected, unless you use a denaturing gel where the strands will be separated. If the latter, then no difference will be seen in the stability of linear or circular DNA once the circular DNA had been relaxed, but the frequency will of course depend on the storage conditions. At minus 20C you will need to wait ~years to see any changes. Higher temperatures and lower pH will accelerate the effects.
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