Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Crystal structure of Δ-[Ru(bpy)2dppz]2+ bound to mismatched DNA reveals side-by-side metalloinsertion and intercalation

Abstract

DNA mismatches represent a novel target in the development of diagnostics and therapeutics for cancer, because deficiencies in DNA mismatch repair are implicated in cancers, and cells that are repair-deficient show a high frequency of mismatches. Metal complexes with bulky intercalating ligands serve as probes for DNA mismatches. Here, we report the high-resolution (0.92 Å) crystal structure of the ruthenium ‘light switch’ complex Δ-[Ru(bpy)2dppz]2+ (bpy = 2,2′-bipyridine and dppz = dipyridophenazine), which is known to show luminescence on binding to duplex DNA, bound to both mismatched and well-matched sites in the oligonucleotide 5′-(dCGGAAATTACCG)2-3′ (underline denotes AA mismatches). Two crystallographically independent views reveal that the complex binds mismatches through metalloinsertion, ejecting both mispaired adenosines. Additional ruthenium complexes are intercalated at well-matched sites, creating an array of complexes in the minor groove stabilized by stacking interactions between bpy ligands and extruded adenosines. This structure attests to the generality of metalloinsertion and metallointercalation as DNA binding modes.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Structure of Δ-[Ru(bpy)2dppz]2+ (1) bound to the oligonucleotide 5′-C1G2G3A4A5A6T7T8A9C10C11G12-3′.
Figure 2: Two independent views of metalloinsertion at the mismatched sites.
Figure 3: Two independent views of metallointercalation at well-matched sites.
Figure 4: The end-capping complex.
Figure 5: Solution luminescence.

Similar content being viewed by others

References

  1. Loeb, L. A. A mutator phenotype in cancer. Cancer Res. 61, 3230–3239 (2001).

    CAS  PubMed  Google Scholar 

  2. Strauss, B. S. Frameshift mutation, microsatellites and mismatch repair. Mutat. Res. 437, 195–203 (1999).

    Article  CAS  Google Scholar 

  3. Papadopoulos, N. & Lindblom, A. Molecular basis of HNPCC: mutations of MMR genes. Hum. Mutat. 10, 89–99 (1997).

    Article  CAS  Google Scholar 

  4. Peltomaki, P. Deficient DNA mismatch repair: a common etiologic factor for colon cancer. Hum. Mol. Genet. 10, 735–740 (2001).

    Article  CAS  Google Scholar 

  5. Lawes, D. A., SenGupta, S. & Boulos, P. B. The clinical importance and prognostic implications of microsatellite instability in sporadic cancer. Eur. J. Surg. Oncol. 29, 201–212 (2003).

    Article  CAS  Google Scholar 

  6. Bhattacharyya, N. P., Skandalis, A., Ganesh, A., Groden, J. & Meuth, M. Mutator phenotypes in human colorectal carcinoma cell lines. Proc. Natl Acad. Sci. USA 91, 6319–6323 (1994).

    Article  CAS  Google Scholar 

  7. Arzimanoglou, I. I., Gilbert, F. & Barber, H. R. K. Microsatellite instability in human solid tumors. Cancer 82, 1808–1820 (1998).

    Article  CAS  Google Scholar 

  8. Boland, C. R. et al. A national cancer institute workshop on microsatellite instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer. Cancer Res. 58, 5248–5257 (1998).

    CAS  PubMed  Google Scholar 

  9. de la Chapelle, A. Microsatellite instability. N. Engl. J. Med. 349, 209–210 (2003).

    Article  Google Scholar 

  10. Rosen, D. G., Cai, K. Q., Luthra, R. & Liu, J. Immunohistochemical staining of hMLH1 and hMSH2 reflects microsatellite instability status in ovarian carcinoma. Mod. Pathol. 19, 1414–1420 (2006).

    Article  CAS  Google Scholar 

  11. Lim, M. H., Song, H., Olmon, E. D., Dervan, E. E. & Barton, J. K. Sensitivity of [Ru(bpy)2dppz]2+ luminescence to DNA defects. Inorg. Chem. 48, 5392–5397 (2009).

    Article  CAS  Google Scholar 

  12. Friedman, A. E., Chambron, J. C., Sauvage, J. P., Turro, N. J. & Barton, J. K. A molecular light switch for DNA: [Ru(bpy)2(dppz)]2+. J. Am. Chem. Soc. 112, 4960–4962 (1990).

    Article  CAS  Google Scholar 

  13. Hiort, C., Lincoln, P. & Norden, B. DNA binding of Δ- and Λ-[Ru(phen)2DPPZ]2+. J. Am. Chem. Soc. 115, 3448–3454 (1993).

    Article  CAS  Google Scholar 

  14. Dupureur, C. M. & Barton, J. K. Use of selective deuteration and 1H NMR in demonstrating major groove binding of Δ-[Ru(phen)2dppz]2+ to d(GTCGAC)2 . J. Am. Chem. Soc. 116, 10286–10287 (1994).

    Article  CAS  Google Scholar 

  15. Haq, I. et al. Interaction of Δ- and Λ-[Ru(phen)2DPPZ]2+ with DNA: a calorimetric and equilibrium binding study. J. Am. Chem. Soc. 117, 4788–4796 (1995).

    Article  CAS  Google Scholar 

  16. Lincoln, P., Broo, A. & Norden, B. Diastereomeric DNA-binding geometries of intercalated ruthenium(II) trischelates probed by linear dichroism: [Ru(phen)2DPPZ]2+ and [Ru(phen)2BDPPZ]2+. J. Am. Chem. Soc. 118, 2644–2653 (1996).

    Article  CAS  Google Scholar 

  17. Dupureur, C. M. & Barton, J. K. Structural studies of Λ- and Δ-[Ru(phen)2dppz]2+ bound to d(GTCGAC)2: characterization of enantioselective intercalation. Inorg. Chem. 36, 33–43 (1997).

    Article  CAS  Google Scholar 

  18. Ambrosek, D., Loos, P.-F., Assfeld, X. & Daniel, C. A theoretical study of Ru(II) polypyridyl DNA intercalators: structure and electronic absorption spectroscopy of [Ru(phen)2(dppz)]2+ and [Ru(tap)2(dppz)]2+ complexes intercalated in guanine–cytosine base pairs. J. Inorg. Biochem. 104, 893–901 (2010).

    Article  CAS  Google Scholar 

  19. Vargiu, A. V. & Magistrato, A. Detecting DNA mismatches with metallo-insertors: a molecular simulation study. Inorg. Chem. 51, 2046–2057 (2012).

    Article  CAS  Google Scholar 

  20. Hall, J. P. et al. Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand. Proc. Natl Acad. Sci. USA 108, 17610–17614 (2011).

    Article  CAS  Google Scholar 

  21. Pierre, V. C., Kaiser, J. T. & Barton, J. K. Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator. Proc. Natl Acad. Sci. USA 104, 429–434 (2007).

    Article  CAS  Google Scholar 

  22. Zeglis, B. M., Pierre, V. C., Kaiser, J. T. & Barton, J. K. A bulky rhodium complex bound to an adenosine–adenosine DNA mismatch: general architecture of the metalloinsertion binding mode. Biochemistry 48, 4247–4253 (2009).

    Article  CAS  Google Scholar 

  23. Cordier, C., Pierre, V. C. & Barton, J. K. Insertion of a bulky rhodium complex into a DNA cytosine–cytosine mismatch: an NMR solution study. J. Am. Chem. Soc. 129, 12287–12295 (2007).

    Article  CAS  Google Scholar 

  24. Zeglis, B. M., Pierre, V. C. & Barton, J. K. Metallo-intercalators and metallo-insertors. Chem. Commun. 44, 4565–4579 (2007).

    Article  Google Scholar 

  25. Holmlin, R. E., Stemp, E. D. A. & Barton, J. K. [Ru(phen)2dppz]2+ luminescence: dependence on DNA sequences and groove-binding agents. Inorg. Chem. 37, 29–34 (1998).

    Article  CAS  Google Scholar 

  26. Sobell, H. M., Tsai, C.-C., Jain, S. C. & Gilbert, S. G. Visualization of drug–nucleic acid interactions at atomic resolution: III. Unifying structural concepts in understanding drug–DNA interactions and their broader implications in understanding protein–DNA interactions. J. Mol. Biol. 114, 333–365 (1977).

    Article  CAS  Google Scholar 

  27. Kielkopf, C. L., Erkkila, K. E., Hudson, B. P., Barton, J. K. & Rees, D. C. Structure of a photoactive rhodium complex intercalated into DNA. Nature Struct. Mol. Biol. 7, 117–121 (2000).

    Article  CAS  Google Scholar 

  28. Adams, A., Guss, J. M., Denny, W. A. & Wakelin, L. P. G. Crystal structure of 9-amino-N-[2-(4-morpholinyl)ethyl]-4-acridinecarboxamide bound to d(CGTACG)2: implications for structure–activity relationships of acridinecarboxamide topoisomerase poisons. Nucleic Acids Res. 30, 719–725 (2002).

    Article  CAS  Google Scholar 

  29. Barton, J. K. Metals and DNA: molecular left-handed complements. Science 233, 727–734 (1986).

    Article  CAS  Google Scholar 

  30. Sigman, D. S. & Chen, C.-H. B. Chemical nucleases: new reagents in molecular biology. Annu. Rev. Biochem. 59, 207–236 (1990).

    Article  CAS  Google Scholar 

  31. Lim, M. H., Lau, I. H. & Barton, J. K. DNA strand cleavage near a CC mismatch directed by a metalloinsertor. Inorg. Chem. 46, 9528–9530 (2007).

    Article  CAS  Google Scholar 

  32. Amouyal, E., Homsi, A., Chambron, J.-C. & Sauvage, J.-P. Synthesis and study of a mixed-ligand ruthenium(II) complex in its ground and excited states: bis(2,2′-bipyridine)(dipyrido[3,2-a:2′,3′-c]phenazine-N4N5)ruthenium(II). J. Chem. Soc. Dalton Trans. 1841–1845 (1990).

  33. Liu, J.-G. et al. Enantiomeric ruthenium(II) complexes binding to DNA: binding modes and enantioselectivity. J. Biol. Inorg. Chem. 5, 119–128 (2000).

    Article  CAS  Google Scholar 

  34. Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010).

    Article  CAS  Google Scholar 

  35. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994).

  36. Sheldrick, G. M. A short history of SHELX. Acta Crystallogr. A 64, 112–122 (2008).

    Article  CAS  Google Scholar 

  37. Emsley, P. & Cowtan, K. COOT: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).

    Article  Google Scholar 

  38. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).

    Article  CAS  Google Scholar 

  39. Schrodinger, LLC. The PyMOL Molecular Graphics System (Schrodinger, 2010).

  40. Kleywegt, G. J. Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr. D 52, 842–857 (1996).

    Article  CAS  Google Scholar 

  41. Lu, X. & Olson, W. K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 31, 5108–5121 (2003).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank S.C. Virgil for assistance in the separation of enantiomers and D.C. Rees and J.A. Hoy for valuable discussions. The authors are grateful to the National Institutes of Health (NIH GM33309 to J.K.B.) for financial support and the Tobacco-Related Disease Research Program (TRDRP) for a Dissertation Research Award to H.S. The authors also acknowledge the Gordon and Betty Moore Foundation and Sanofi-Aventis Bioengineering Research Program at Caltech for support of the X-ray Facility at Caltech Molecular Observatory. The rotation camera facility at Stanford Synchrotron Radiation Laboratory is supported by the US Department of Energy and the NIH.

Author information

Authors and Affiliations

Authors

Contributions

J.K.B. and H.S. designed the research. H.S. carried out crystallization and solution luminescence experiments. J.T.K. and H.S. solved the crystal structure. H.S. and J.K.B. wrote the manuscript.

Corresponding author

Correspondence to Jacqueline K. Barton.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary information (PDF 872 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Song, H., Kaiser, J. & Barton, J. Crystal structure of Δ-[Ru(bpy)2dppz]2+ bound to mismatched DNA reveals side-by-side metalloinsertion and intercalation. Nature Chem 4, 615–620 (2012). https://doi.org/10.1038/nchem.1375

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchem.1375

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing