3. Clevage reaction: The closed complex activates the clevage activity of the enzyme resulting into the introduction of DNA break on both strand to give fragment with 3’OH and a 5’-phosphate group.

Distinction between self Vs Foreign DNA: Although the precise mechanism of distinction is not known but based on availble literature, in the absence of methylation a closed complex is formed and it allowes proper activation of clevage activity of the enzyme. But presence of the methyl group (even hemi-methylation) on nucleotide does not allow formation of closed complex and consequently enzyme falls from the DNA.

Figure 14.3: Proposed mechanism of Type II Restricton enzyme catalysis