Why does my McrBC cleaved DNA smear when run on an agarose gel?

McrBC makes one cut between each pair of half-sites, cutting close to one half-site or the other, but cleavage positions are distributed over several base pairs approximately 30 base pairs from the methylated base (1). Therefore, when multiple McrBC half-sites are present in DNA (as is the case with cytosine-methylated genomic DNA) the flexible nature of the recognition sequence results in an overlap of sites, producing a smeared rather than a sharp banding pattern.
(1) Stewart, F. J. and Raleigh E. A. (1998) Biol. Chem. 379, 611-616.

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