Structural specificities of five commonly used DNA nucleases

Five commonly used nucleases were surveyed for their ability to distinguish among several different DNA backbone configurations. The digestion data suggest that: (1) DNAase I binds across the minor groove; whereas (2) nuclease S1 and (3) micrococcal nuclease bind to an exposed single strand; (4) copper/phenanthroline seeks a base-pair step; and (5) DNAase II requires just a stacked single strand of limited exposure. Only micrococcal nuclease is demonstrably base-specific, with a strong preference for T, A over C, G in any structural context.