DNA recognition by DNase I

Bovine pancreatic DNase I shows a strong preference for double-stranded substrates and cleaves DNA with strongly varying cutting rates suggesting that the enzyme recognises sequence-dependent structural variations of the DNA double helix. The complicated cleavage pattern indicates that several local as well as global helix parameters influence the cutting frequency of DNase I at a given bond. The high resolution crystal structures of two DNase I-DNA complexes showed that the enzyme binds tightly in the minor groove, and to the sugar-phosphate backbones of both strands, and thereby induces a widening of the minor groove and a bending towards the major groove. In agreement with biochemical data this suggests that flexibility and minor groove geometry are major parameters determining the cutting rate of DNase I. Experimental observations showing that the sequence environment of a dinucleotide step strongly affects its cleavage efficiency can be rationalized by the fact that six base pairs are in contact with the enzyme. Mutational analysis based on the structural results has identified critical residues for DNA binding and cleavage and has lead to a proposal for the catalytic mechanism.