Type II restriction endonucleases recognize specific DNA sequences, typically 4–8 bp in length, and cleave phosphodiester bonds in the presence of Mg2+, within or close to their recognition sites (Pingoud and Jeltsch 2001). Around 3500 species, from variety of bacteria with nearly 240 differing specificities, have now been characterized (Roberts et al. 2003). Most of the sequences recognized by Type II restriction endonucleases are palindromic, i. e., possess a twofold rotational axis of symmetry. On the basis of this observation, Kelly and Smith proposed the first model for the interaction of these restriction enzymes with DNA (Kelly and Smith 1970).According to their model (Fig. 1), recognition of the palindromic DNA sequence is achieved by two identical protein subunits related by a twofold axis of symmetry. Each subunit faces the same nucleotide sequence on the opposite DNA strand and contains one active site. Symmetrical nicking of opposite DNA strands by both monomers within a homodimer generates the double-strand break. Hence, the symmetry of the recognition sequence implies the oligomeric state of the restriction enzyme.