The artificial nuclease activity of (OP),Cu+ and H202 has been used to analyze the DNA conformation of single-stranded DNA from the coliphage M-13, and the B-type DNA of the promoter region of the lac operon. Despite the strong kinetic preference of the reaction of B-DNA, demonstrated with synthetic polynucleotides, the reagent cannot distinguish the double-stranded hairpin turns in M-13 from the extensive single-stranded region because the latter forms metastable hydrogen-bonded structures that are readily cleaved.
Analyses of the promoter regions of the lac operon of the wild-type and of the P, and UV-5 mutations have demonstrated that the promoter-specific sequence (Pribnow Box), extending from positions -12 to -6, exhibits a characteristic hyperreactivity to the reagent. The wild-type DNA has hypersensitive sites at the boundary of this region, at positions -13 and -12. The P, and UV-5 mutations, which support cyclic AMP proteinindependent transcription, have mutations at -9, and -9 and -8, respectively, and possess additional hyperreactive sites calibrated at -11 and -10 in the sequence. These experiments demonstrate that the local structure of the DNA in these control regions is different. The unique structure of the promoter may govern recognition of the DNA by RNA polymerase. The artificial nuclease activity of (OP),Cu+ may therefore be useful to identify functionally significant local variations in DNA structure.