Structure subtraction as an approach to investigation of the mechanism of restriction enzyme action.

Endonuclease BamHI cleaves the phosphodiester bonds between the guanine residues within the duplex DNA sequence G decreases GATCC. The substrate characteristics of oligonucleotides, containing some defects in the sequence recognized by endonuclease (nick, absence of some internucleotide phosphate or nucleotide, partially single-stranded form of the recognition site) were investigated. The results suggest that the specificity of synthetic oligonucleotide cleavage is strongly dependent on the ribosophosphate backbone intactness inside the recognition site. BamHI was found not to hydrolyse the phosphodiester bonds outside the double helix. Also BamHI forms a productive complex with the non-symmetrical substrate, having half the recognition sites, of a single strand.