In a plasmid maxi prep, many a times, nicked circular species are isolated apart from supercoiled. Can this nick be rejoined by incubating the prep with ligase? I know it won't increase supercoiled plasmid per se, but, can it be used to at least eliminate the nicked plasmids? Will it be safe to use?
If you want to eliminate the nicks then yes, that will work. Just remember that formerly nicked molecules will remain in a "relaxed" conformation i.e. no supercoiling.
Out of curiosity, why is it that you want to reseal nicks?
The short answer is YES. However, you can reduce the percentage of "nicked" form of plasmid DNA significantly by gently mixing the bacterial lysate and reducing the DNA denaturation time from 5 min to 4 min. Both may increase the proportion of supercoiled DNA. However, it would reduce the plasmid DNA yield.
In principle nicked plasmid form work like un-nicked forms for any further molecular experiment.
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