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Structure of a photoactive rhodium complex intercalated into DNA

Nature Structural Biology volume 7, pages 117–121 (2000)Cite this article

Abstract

Intercalating complexes of rhodium(III) are strong photo-oxidants that promote DNA strand cleavage or electron transfer through the double helix. The 1.2 Å resolution crystal structure of a sequence-specific rhodium intercalator bound to a DNA helix provides a rationale for the sequence specificity of rhodium intercalators. It also explains how intercalation in the center of an oligonucleotide modifies DNA conformation. The rhodium complex intercalates via the major groove where specific contacts are formed with the edges of the bases at the target site. The phi ligand is deeply inserted into the DNA base pair stack. The primary conformational change of the DNA is a doubling of the rise per residue, with no change in sugar pucker from B-form DNA. Based upon the five crystallographically independent views of an intercalated DNA helix observed in this structure, the intercalator may be considered as an additional base pair with specific functional groups positioned in the major groove.

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Figure 1: Overall structure of the rhodium complex bound to the DNA oligonucleotide 5′-G(dIU)TGCAAC-3′.
Figure 2: Sequence-specific interactions between the rhodium complex and the DNA major groove.

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Acknowledgements

We are grateful to the NIH for research support and to the NSF and NIH for predoctoral fellowships to C.L.K and K.E.E. We thank L. Joshua-Tor, S.S. David, J.E. Wedekind, A.J. Chirino and R. Bau for assistance with the structure solution, and S. Horvath for oligonucleotide synthesis. The rotation camera facility at SSRL is supported by the U.S. Department of Energy and NIH.

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Author notes

  1. Clara L. Kielkopf

    Present address: Department of Molecular Biophysics, The Rockefeller University, New York, New York, 10021, USA

  2. Brian P. Hudson

    Present address: Department of Chemistry, Scripps Research Institute, La Jolla, California, 92037, USA

Authors and Affiliations

  1. Division of Biology, California Institute of Technology, Pasadena, 91125, California, USA

    Clara L. Kielkopf

  2. Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, 91125, California, USA

    Kathryn E. Erkkila, Brian P. Hudson, Jacqueline K. Barton & Douglas C. Rees

  3. Howard Hughes Medical Institute, California Institute of Technology, Pasadena, 91125, California, USA

    Douglas C. Rees

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  1. Clara L. Kielkopf
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  5. Douglas C. Rees
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Corresponding authors

Correspondence to Jacqueline K. Barton or Douglas C. Rees.

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Kielkopf, C., Erkkila, K., Hudson, B. et al. Structure of a photoactive rhodium complex intercalated into DNA. Nat Struct Mol Biol 7, 117–121 (2000). https://doi.org/10.1038/72385

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