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Nucleic Acids Research, 1988, Vol. 16, No. 16 7943-7960
© 1988

Articles

Rh(DIP)33+: a shape-selective metal complex which targets cruciforms

Mindy R. Kirshenbaum, Roger Tribolet and Jacqueline K. Barton*

Department of Chemistry, Columbia University New York, NY 10027, USA

*To whom correspondence should be addressed

Received April 28, 1988. Revised July 20, 1988. Accepted July 20, 1988.

The coordination complex tris(4,7-diphenylphenanthroline)rhodium(III), Rh(DIP)33+ binds to and, upon photoactivation, cleaves both DNA strands near the base of a DNA cruciform Sites of photoinduced double-stranded DNA cleavage by the rhodium complex map to regions containing cruciforms on closed circular pBR322, pColE1 and {varphi}X174 (replicative form) DNAs. Neither cleavage nor binding by the metal complex, assayed using S1 nuclease, is found on the linear plasmid which lacks the extruded cruciform. High resolution mapping experiments reveal that h(DIP)33+ cleaves at a specific AT-rich site neighboring the stem of the minor cruciform on pBR322. The primary site of cleavage is found at position 3238 on the 3'-strand and 3250 on the 5-strand and is remarkably specific. The pattern of cleavage, to one side only of the cruciform stem, indicates an asymmetry in the cruciform structure recognized by the complex. These results suggest that Rh(DIP)33+ may provide a useful reagent to probe cruciform sites. In addition, the high degree of specificity found in targeting the cruciform structure with this simple metal complex underscores the utility of shape-selection for the recognition of specific sites on a DNA strand.


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