Novel properties of a restriction endonuclease isolated from Haemophilus parahaemolyticus

The sequences in lambda DNA in and around six sites cut by Hph, a restriction enzyme isolated from Haemophilus parahaemolyticus, are compared. The enzyme produces a staggered cut around an AT or TA base pair, but the sequences immediately surroinding the cleavage sites bear no obvious relation to one another. Eight (in some cases nine) base pairs to one side of each cleavage site is the common sequence TCACC AGTGG. Two lines of evidence indicate that these bases constitute part or all of the Hph recognition site. First, mutations in this sequence prevent Hph cutting. Second, dimethylsulfate-mediated methylation of Gs and As in this site prevent cutting, whereas methylation of purines in the region between this sequence and the cleavage sites has no such effect. There is discernible 2-fold rotational symmetry neither in the common sequence nor around the cleavage sites.