Is extended digestion using SfaNI recommended?

No, the DNA may get degraded. TypeIIs enzymes such as SfaNI will often yield worse results if more enzyme is added than is necessary or if digestion longer than one hour is attempted. This effect is not due to a contaminating nuclease, but instead to inherent additional activities of the SfaNI enzyme. Because this enzyme is composed of distinct recognition and cleavage moieties, random degradation of the protein during a long digest will occasionally release an active cleavage moiety which is no longer regulated by the recognition moiety. Thus, long digests will result in the creation of nuclease. This property is not the same as Star Activity.

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