Unfortunately we don't know exactly what ends McrBC leaves. There may even be a mixture of types of ends produced. If McrBC digestion products are to be ligated, we suggest treating the McrBC-digested DNA with Klenow Fragment (3´→5´ exo-) (NEB #M0212) or T4 DNA polymerase (NEB #M0203). This enzyme will remove 3' overhangs and fill-in 5' overhangs, while leaving blunt ends alone. This should leave you with only blunt ends, which could then be ligated.
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