The binding modes of a rationally designed photoactivated DNA nuclease determined by NMR

The complex between the rationally designed synthetic DNA cleaving agent netropsin-diazene and the double-stranded DNA ollgomer 5′-CGCAAAAGGC-3′.5′-GCCTTTTGCG-3′ was characterized by two-dimensional NMR spectroscopy in solution. Photolysis of netropsin-diazene bound to DNA generates a trimethylenemethane diradlcal intermediate that induces single-strand breaks in the DNA. The π-dlyl trimethylenemethane based compounds are a new class of DNA nucleases. We tested the following design criteria: (i) binding of the diazene and subsequent reactive diyl to the DNA, (ii) sequence selectivity in the ligand binding and (iii) prevention of dlyl dimerization. Sixteen NOE derived, ligand-DNA distance restraints were used to obtain the energy minimized model of the complex. The llgand Is bound to the minor groove of the ollgomer with the diazene at the 5′ end of the A-tract in the predominant conformation of the complex. This form of the complex exchanges with a minor conformation In which the ligand is in the opposite orientation. The DNA maintains a B-form structure. Netropsin-diazene has fulfilled all of the design criteria, binding to the DNA duplex studied in the minor groove of the central AAAA tract in a 1:1 mode, preventing diyl dimerization and other side reactions from occurring.