A possible correlation between DNA conformation and the mode of action of restriction enzymes

The cutting modes of restriction endonucleases which recognize tetradeoxyribonucleotide sequences are classified into two groups. d(GGCC) and d(CGCG), for example, are cut to produce blunt ends, while d(CCGG) and d(GCGC) are cut to produce two-base-long cohesive ends. A conformational analysis by the Calladine-Dickerson method indicates that d(GGCC) and d(CGCG) should have a roll angle of successive base-pairs open towards the major groove at the central (second) base-pair step. On the other hand, d(CCGG) and d(GCGC) have such open roll angles at the first and third base-pair steps. It is suggested that, in general, the cutting mode of a tetramer-specific enzyme depends primarily upon the substrate conformation, rather than upon the enzyme. Similar correlations between the mode of action and substrate conformation are also suggested for hexamer-specific enzymes.