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

H. Peter Spielmann, Patricia A. Fagan, Therese M. Bregant, R. Daniel Little, David E. Wemmer

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


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.

Original languageEnglish
Pages (from-to)1576-1583
Number of pages8
JournalNucleic Acids Research
Issue number9
StatePublished - May 11 1995

Bibliographical note

Funding Information:
This work was supported in part by the National Institutes of Health grant GM^3219 (DEW), postdoctoral fellowship GM-14966 (HPS) and through instrumentation grants from the US Department of Energy, DE FGO5-86ER75281 and the National Science Foundation, DMB 86-09305 and BBS 87-20134 and by the Director, Office of Biological and Environmental Research, General Sciences Division of the US Department of Energy under Contract No. DE-AC03-76SF00098 (DEW). RDL and TMB are very grateful to the NIH (Public Health Service, National Cancer Institute Grant CA58323) for their support of our effort

ASJC Scopus subject areas

  • Genetics


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