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.

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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.

References

  1. 1

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

  2. 2

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

  3. 3

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

  4. 4

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

  5. 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).

  6. 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).

  7. 7

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

  8. 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).

  9. 9

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

  10. 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).

  11. 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).

  12. 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).

  13. 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).

  14. 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).

  15. 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).

  16. 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).

  17. 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).

  18. 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).

  19. 19

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

  20. 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).

  21. 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).

  22. 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).

  23. 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).

  24. 24

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

  25. 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).

  26. 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).

  27. 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).

  28. 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).

  29. 29

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

  30. 30

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

  31. 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).

  32. 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. 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).

  34. 34

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

  35. 35

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

  36. 36

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

  37. 37

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

  38. 38

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

  39. 39

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

  40. 40

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

  41. 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).

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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

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.

Correspondence to Jacqueline K. Barton.

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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

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