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

Nature Chemistry

Volumn 4, Issue 8, 2012, Pages 615-620

  Song, Hang ^a   Kaiser, Jens T ^a   Barton, Jacqueline K ^a  

^a California Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COORDINATION COMPOUND; DIPYRIDO(3,2 A 2',3' C)PHENAZINE; DIPYRIDO(3,2-A-2',3'-C)PHENAZINE; DNA; INTERCALATING AGENT; PHENAZINE DERIVATIVE; PYRIDINE DERIVATIVE; RUTHENIUM;

ARTICLE; BASE MISPAIRING; CHEMICAL STRUCTURE; CHEMISTRY; X RAY CRYSTALLOGRAPHY;

BASE PAIR MISMATCH; COORDINATION COMPLEXES; CRYSTALLOGRAPHY, X-RAY; DNA; INTERCALATING AGENTS; MODELS, MOLECULAR; PHENAZINES; PYRIDINES; RUTHENIUM;

EID: 84864335633     PISSN: 17554330     EISSN: 17554349     Source Type: Journal    
DOI: 10.1038/nchem.1375     Document Type: Article

References (41)

1. Loeb, L. A. A mutator phenotype in cancer. Cancer Res. 61, 3230-3239 (2001). (Pubitemid 32695004)
2. Strauss, B. S. Frameshift mutation, microsatellites and mismatch repair. Mutat. Res. 437, 195-203 (1999).
3. Papadopoulos, N. & Lindblom, A. Molecular basis of HNPCC: Mutations of MMR genes. Hum. Mutat. 10, 89-99 (1997). (Pubitemid 27327483)
4. Peltomaki, P. Deficient DNA mismatch repair: A common etiologic factor for colon cancer. Hum. Mol. Genet. 10, 735-740 (2001). (Pubitemid 32331582)
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). (Pubitemid 36395552)
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). (Pubitemid 24200652)
7. Arzimanoglou, I. I., Gilbert, F. & Barber, H. R. K. Microsatellite instability in human solid tumors. Cancer 82, 1808-1820 (1998). (Pubitemid 28208635)
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). (Pubitemid 28521189)
9. de la Chapelle, A. Microsatellite instability. N. Engl. J. Med. 349, 209-210 (2003).
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). (Pubitemid 44624159)
11. 2+ luminescence to DNA defects. Inorg. Chem. 48, 5392-5397 (2009).
12. 2+. J. Am. Chem. Soc. 112, 4960-4962 (1990). (Pubitemid 20285921)
13. 2+. J. Am. Chem. Soc. 115, 3448-3454 (1993).
14. 2+ to d(GTCGAC)2. J. Am. Chem. Soc. 116, 10286-10287 (1994). (Pubitemid 24981816)
15. Haq, I. et al. Interaction of D- And L-[Ru(phen)2DPPZ]2+ with DNA: A calorimetric and equilibrium binding study. J. Am. Chem. Soc. 117, 4788-4796 (1995).
16. 2+. J. Am. Chem. Soc. 118, 2644-2653 (1996).
17. 2+ bound to d(GTCGAC)2: Characterization of enantioselective intercalation. Inorg. Chem. 36, 33-43 (1997). (Pubitemid 127483598)
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. Vargiu, A. V. & Magistrato, A. Detecting DNA mismatches with metalloinsertors: A molecular simulation study. Inorg. Chem. 51, 2046-2057 (2012).
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. 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). (Pubitemid 46123043)
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. 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). (Pubitemid 47556864)
24. Zeglis, B. M., Pierre, V. C. & Barton, J. K. Metallo-intercalators and metalloinsertors. Chem. Commun. 44, 4565-4579 (2007).
25. Holmlin, R. E., Stemp, E. D. A. & Barton, J. K. Ru(phen)2dppz2+ luminescence: Dependence on DNA sequences and groove-binding agents. Inorg. Chem. 37, 29-34 (1998). (Pubitemid 128487962)
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). (Pubitemid 8142319)
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). (Pubitemid 30082508)
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). (Pubitemid 34679637)
29. Barton, J. K. Metals and DNA: Molecular left-handed complements. Science 233, 727-734 (1986). (Pubitemid 16016223)
30. Sigman, D. S. & Chen, C.-H. B. Chemical nucleases: New reagents in molecular biology. Annu. Rev. Biochem. 59, 207-236 (1990).
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. 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). (Pubitemid 30120595)
34. Kabsch, W. XDS. Acta Crystallogr. D 66, 125-132 (2010).
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).
37. Emsley, P. & Cowtan, K. COOT: Model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004). (Pubitemid 41742764)
38. Adams, P. D. et al. PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213-221 (2010).
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). (Pubitemid 27064310)
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). (Pubitemid 37441878)