Why is some plasmid DNA only partially cut by restriction enzymes such as BclI, ClaI, or XbaI?
These enzymes are known to be inhibited (blocked) by methylation of adenosine (DAM) or cytosine (DCM) residues within their recognition site. The methylations are caused by site specific methylases (DAM or DCM) in the E. coli host, e.g. strains such as DH1, HB101, and JM109. DAM methylates at the adenine in the sequence GATC and DCM methylates at the second cytosine within CCWGG. Inhibition is context specific, so not all methylated recognition sites are blocked, but only those having the methylated residue in close proximity to the protein binding site. One way to overcome problems with methylated restriction sites is to (re)transform a dam-/dcm- strain such as JM110 or DM1 with the respective plasmid and use DNA isolated from this strain for the particular restriction reactions. Most, if not all, enzyme suppliers give appropiate comments in their product data sheets or in their catalogs. Some suppliers even include charts and/or tables of methylation sensitivity. Restriction enzymes
