Cross-links of quadruplex structures from human telomeric DNA by dinuclear platinum complexes show the flexibility of both structures

Biochemistry

Volumn 44, Issue 31, 2005, Pages 10620-10634

  Ourliac Garnier, Isabelle ^a   Elizondo Riojas, Miguel Angel ^b   Redon, Sophie ^a,d   Farrell, Nicholas P ^c   Bombard, Sophie ^a  

^a UNIVERSITÉ PARIS DESCARTES   (France)

^b HOSPITAL UNIVERSITARIO DR JOSÉ ELEUTERIO GONZÁLEZ   (Mexico)

^c VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^d SWISS INST FOR EXP CANCER RESEARCH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CONFORMATIONS; CROSSLINKING; IONS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; PLATINUM COMPOUNDS; SODIUM COMPOUNDS; SOLUTIONS;

DINUCLEAR PLATNIUM COMPLEXES; HUMAN TELOMERIC DNA; QUADRUPLEX STRUCTURES;

DNA;

ADENINE; CATION; DNA; DNA BASE; EXONUCLEASE; GUANINE DERIVATIVE; PLATINUM COMPLEX; POTASSIUM ION; SODIUM ION; SOLVENT;

ARTICLE; COMPLEX FORMATION; DNA CROSS LINKING; DNA STRUCTURE; HUMAN; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; STRUCTURE ANALYSIS;

BINDING SITES; CATIONS, MONOVALENT; COMPUTER SIMULATION; CROSS-LINKING REAGENTS; DNA; DNA ADDUCTS; GUANINE; HUMANS; MODELS, MOLECULAR; ORGANOPLATINUM COMPOUNDS; POTASSIUM; SODIUM; SOLUTIONS; SOLVENTS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; SULFURIC ACID ESTERS; TELOMERE; THERMODYNAMICS;

EID: 23244433818     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050144w     Document Type: Article

References (58)

1. Neidle, S., and Parkinson, G. N. (2003) The structure of telomeric DNA, Curr. Opin. Struct. Biol. 13, 275-283.
2. Wright, W. E., Tesmer, V. M., Huffman, K. E., Levene, S. D., and Shay, J. W. (1997) Normal human chromosomes have long G-rich telomeric overhangs at one end, Genes Dev. 11, 2801-2809.
3. Usdin, K. (1998) NGG-triplet repeats form similar intrastrand structures: Implications for the triplet expansion diseases, Nucleic Acids Res. 26, 4078-4085.
4. Simonsson, T., Pecinka, P., and Kubista, M. (1998) DNA tetraplex formation in the control region of c-myc, Nucleic Acids Res. 26, 1167-1172.
5. Gilbert, D. E., and Feigon, J. (1999) Multistranded DNA structures, Curr. Opin. Struct. Biol. 9, 305-314.
6. Schaffitzel, C., Berger, I., Postberg, J., Hanes, J., Lipps, H. J., and Pluckthun, A. (2001) In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei, Proc. Natl. Acad. Sci. U.S.A. 98, 8572-8577.
7. Neidle, S., and Read, M. A. (2000) G-Quadruplexes as therapeutic targets, Biopolymers 56, 195-208.
8. Arthanari, H., and Bolton, P. H. (2001) Functional and dysfunctional roles of quadruplex DNA in cells, Chem. Biol. 8, 221-230.
9. Siddiqui-Jain, A., Grand, C. L., Bearss, D. J., and Hurley, L. H. (2002) Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription, Proc. Natl. Acad. Sci. U.S.A. 99, 11593-11598.
10. Mergny, J. L., Riou, J. F., Mailliet, P., Teulade-Fichou, M. P., and Gilson, E. (2002) Natural and pharmacological regulation of telomerase, Nucleic Acids Res. 30, 839-865.
11. Rezler, E. M., Bearss, D. J., and Hurley, L. H. (2002) Telomeres and telomerases as drug targets, Curr. Opin. Pharmacol. 2, 415-423.
12. Hud, N. V., Schultze, P., Sklenar, V., and Feigon, J. (1999) Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex, J. Mol. Biol. 285, 233-243.
13. Phillips, K., Dauter, Z., Murchie, A. I., Lilley, D. M., and Luisi, B. (1997) The crystal structure of a parallel-stranded guanine tetraplex at 0.95 A resolution, J. Mol. Biol. 273, 171-182.
14. Simonsson, T. (2001) G-quadruplex DNA structures: Variations on a theme, Biol. Chem. 382, 621-628.
15. 3] G-tetraplex, Structure 1, 263-282.
16. Parkinson, G. N., Lee, M. P., and Neidle, S. (2002) Crystal structure of parallel quadruplexes from human telomeric DNA, Nature 417, 876-880.
17. Balagurumoorthy, P., and Brahmachari, S. K. (1994) Structure and stability of human telomeric sequence, J. Biol. Chem. 269, 21858-21869.
18. Ren, J., Qu, X., Trent, J. O., and Chaires, J. B. (2002) Tiny telomere DNA, Nucleic Acids Res. 30, 2307-2315.
19. + solutions, Nucleic Acids Res. 31, 1605-1613.
20. Lepre, C. A., and Lippard, S. J. (1990) Interaction of platinum antitumor compounds with DNA, Nucleic Acids Mol. Biol. 4, 9-38.
21. Ying, L., Green, J. J., Li, H., Klenerman, D., and Balasubramanian, S. (2003) Studies on the structure and dynamics of the human telomeric G quadruplex by single-molecule fluorescence resonance energy transfer, Proc. Natl. Acad. Sci. U.S.A. 100, 14629-14634.
22. Farrell, N., Qu, Y., Bierbach, U., Valsecchi, M., and Menta, E. (1999) Structure-Activity Relationships within Di- and Trinuclear Platinum Phase-I Clinical Anticancer Agents, in Cisplatin: Chemistry and biochemistry of a leading anticancer drug (Lippert, B., Ed.) pp 479-496, Wiley-VCH, Zurich.
23. Burstyn, J. N., Heiger-Bernays, W. J., Cohen, S. M., and Lippard, S. J. (2000) Formation of cis-diamminedichloroplatinum(II) 1,2-intrastrand cross-links on DNA is flanking-sequence independent, Nucleic Acids Res. 28, 4237-4243.
24. Kasparkova, J., Farrell, N., and Brabec, V. (2000) Sequence specificity, conformation, and recognition by HMG1 protein major DNA interstrand cross-links of antitumor dinuclear platinum complexes, J. Biol. Chem. 275, 15789-15798.
25. Farrell, N., Qu, Y., Feng, L., and Van Houten, B. (1990) Comparison of Chemical Reactivity, Cytotoxicity, Interstrand Cross-Linking and DNA Sequence Specificity of Bis(platinium) Complexes Containing Monodentate or Bidentate Coordination Spheres with Their Monomeric Analogues, Biochemistry 29, 9522-9531.
26. Reeder, F., Kozelka, J., and Chottard, J. C. (1996) Triammine- platinum(II) Coordinated to a Guanine Does Not Prevent Platination of an Adjacent Guanine in Single-Stranded Oligonucleotides, Inorg. Chem. 35, 1413-1415.
27. Kasparkova, J., Mellish, K. J., Qu, Y., Brabec, V., and Farrell, N. (1996) Site-specific d(GpG) intrastrand cross-links formed by dinuclear platinum complexes. Bending and NMR studies, Biochemistry 35, 16705-16713.
28. Zou, Y., Van Houten, B., and Farrell, N. (1994) Sequence specificity of DNA-DNA interstrand cross-link formation by cisplatin and dinuclear platinum complexes, Biochemistry 33, 5404-5410.
29. 4 telomeric sequence: A structural and cross-linking study, Biochemistry 40, 8463-8470.
30. Case, D. A., Pearlman, D. A., Caldwell, J. M., Cheatman, T. E., III, Wang, J., Ross, W. S., Simmerling, C. L., Darden, T. A., Merz, K. M., Stanton, R. V., Cheng, A. L., Vincent, J. J., Crowley, M., Tsui, V., Gohlke, H., Radmer, R. J., Duan, Y., Pitera, J., Massova, I., Seibel, G. L., Singh, U. C., Weiner, P. K., and Kollman, P. A. (2002) AMBER 7.0, University of California, San Francisco.
31. Tsui, V., and Case, D. A. (2000) Molecular dynamics simulations of nucleic acids with a generalized Born solvation model, J. Am. Chem. Soc. 122, 2489-2498.
32. Cheatham, T. E., Cieplack, I. P., and Kollman, P. A. (1999) A modifed version of the Cornell et al. force field with improved sugar pucker phases and helical repeat, J. Biomol. Struct. Dyn. 4, 845-862.
33. Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: Visual Molecular Dynamics, J. Mol. Graphics 14.1, 33-38.
34. 2+, Angew. Chem., Int. Ed. 41, 2998-3001.
35. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Montgomery, J. J. A., Vreven, T., Kudin, K. N., Burant, J. C., Millam, J. M., Iyengar, S. S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G. A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J. E., Hratchian, H. P., Cross, J. B., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Ayala, P. Y., Morokuma, K., Voth, G. A., Salvador, P., Dannenberg, J. J., Zakrzewski, V. G., Dapprich, S., Daniels, A. D., Strain, M. C., Farkas, O., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Ortiz, J. V., Cui, Q., Baboul, A. G., Clifford, S., Cioslowski, J., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Gonzalez, C., and Pople, J. A. (2003) Gaussian 03, Gaussian, Inc., Pittsburgh, PA.
36. Besler, B. H., Merz, K. M. J., and Kollman, P. A. (1990) Atomic charges derived from semiempirical methods, J. Comput. Chem. 11, 431-439.
37. Ellis, L. T., and Hambley, T. W. (1994) Dichloro(ethylenediamine) platinum(II), Acta Crystallogr. C50, 1888-1889.
38. 3, Acta Crystallogr. C50, 1217-1220.
39. Michalska, D., and Wysokinski, R. (2004) Molecular Structure and Bonding in Platinum-Picoline Anticancer Complex: Density Functional Study, Collect. Czech. Chem. Commun. 69, 63-71.
40. Herman, F., Kozelka, J., Sloven, V., Guittet, E., Girault, J. P., Huynh-Dinh, T., Igolen, J., Lallemand, J. Y., and Chottard, J. C. (1990) A d(GpG)-platinated decanucleotide duplex is kinked: An extended NMR and molecular mechanics study, Eur. J. Biochem. 194, 119-133.
41. Elizondo-Riojas, M.-A., Gonnet, F., Auge-Barrere-Mazouat, P., Allain, F., Berges, J., Attias, R., Chottard, J. C., and Kozelka, J. (1997) Molecular modeling of platinum complexes with oligonucleotides: Methodological lessons and structural insights, in Molecular Modeling and Dynamics of Bioinorganic Systems (Banci, L., and Comba, P., Eds.) pp 131-160, Kluwer Academic Publishers, Dordrecht, The Netherlands.
42. Chval, Z., and Síp, M. (1998) Force field for platinum binding to adenine and guanine taking into account flexibility of nucleic acids bases, J. Phys. Chem. 102, 1659-1661.
43. Phan, A. T., and Mergny, J. L. (2002) Human telomeric DNA: G-Quadruplex, i-motif and Watson-Crick double helix, Nucleic Acids Res. 30, 4618-4625.
44. Henderson, E. R., Moore, M., and Malcolm, B. A. (1990) Telomere G-strand structure and function analyzed by chemical protection, base analogue substitution, and utilization by telomerase in vitro, Biochemistry 29, 732-737.
45. Stefl, R., Spackova, N., Berger, I., Koca, J., and Sponer, J. (2001) Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine, Biophys. J. 80, 455-468.
46. Bombard, S., Favre, A., and Kozelka, J. (1998) Very short oligonucleotides migrate on 20% polyacrylamide gels with an apparent friction coefficient proportional to molecular mass, Anal. Biochem. 263, 123-125.
47. Escaffre, M., Favre, A., Chottard, J. C., and Bombard, S. (2002) Determination of platinated purines in oligoribonucleotides by limited digestion with ribonucleases T1 and U2, Anal. Biochem. 310, 42-49.
48. Seenisamy, J., Rezler, E. M., Powell, T. J., Tye, D., Gokhale, V., Joshi, C. S., Siddiqui-Jain, A., and Hurley, L. H. (2004) The dynamic character of the G-quadruplex element in the c-MYC promoter and modification by TMPyP4, J. Am. Chem. Soc. 126, 8702-8709.
49. He, Y. J., Neumann, R. D., and Panyutin, I. G. (2004) Intramolecular quadruplex conformation of human telomeric DNA assessed with I-125-radioprobing, Nucleic Acids Res. 32, 5359-5367.
50. Phan, A. T., and Patel, D. J. (2003) Two-repeat human telomeric d(TAGGGTTAGGGT) sequence forms interconverting parallel and antiparallel G-quadruplexes in solution: Distinct topologies, thermodynamic properties, and folding/unfolding kinetics, J. Am. Chem. Soc. 125, 15021-15027.
51. 4), FEBS Lett. 496, 128-133.
52. 2+, Nucleic Acids Res. 31, 1156-1163.
53. Hardin, C. C., Corregan, M. J., Lieberman, D. V., and Brown, B. A., II (1997) Allosteric interactions between DNA strands and monovalent cations in DNA quadruplex assembly: Thermodynamic evidence for three linked association pathways, Biochemistry 36, 15428-15450.
54. Mergny, J. L., Phan, A. T., and Lacroix, L. (1998) Following G-quartet formation by UV-spectroscopy, FEBS Lett. 435, 74-78.
55. 1H NMR, Biochemistry 35, 15383-15390.
56. Phan, A. T., Modi, Y. S., and Patel, D. J. (2004) Two-repeat Tetrahymena Telomeric d(TGGGGTTGGGGT) Sequence Interconverts Between Asymmetric Dimeric G-quadruplexes in Solution, J. Mol. Biol. 338, 93-102.
57. 2+ by enzymatic degradation of the products and ESI and MALDI mass spectrometries, J. Mass Spectrum. 31, 802-809.
58. Guittard, J., Pacifico, C., Blais, J. C., Bolbach, G., Chottard, J. C., and Spassky, A. (1995) Matrix-assisted laser desorption ionization time-of-flight mass spectrometry of DNA-Pt(II) complexes, Mass Spectrom. 9, 33-36.