Intercalative G-tetraplex stabilization of telomeric DNA by a cationic porphyrin

Journal of the American Chemical Society

Volumn 121, Issue 9, 1999, Pages 1768-1779

  Haq, Ihtshamul ^a,c   Trent, John O ^b   Chowdhry, Babur Z ^a   Jenkins, Terence C ^a  

^a UNIVERSITY OF GREENWICH   (United Kingdom)

^b University of Alabama at Birmingham   (United States)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PORPHYRIN; POTASSIUM ION;

ARTICLE; CALORIMETRY; CILIATE; INTERCALATION COMPLEX; MOLECULAR MODEL; PROTEIN ASSEMBLY; PROTEIN DNA BINDING; SPECTROPHOTOMETRY; STOICHIOMETRY; TELOMERE;

EID: 0033541133     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja981554t     Document Type: Article

References (67)

1. 2TMPyP, 5,10,15,20-tetrakis(1-methyl-4-pyridyl)-21H-porphine; ITC, isothermal titration calorimetry; MD, molecular dynamics.
2. (a) Blackburn, E. H. Nature 1991, 350, 569-573.
3. (b) Kang, C. H.; Zhang, X.; Ratliff, R.; Moyzis, R.; Rich, A. Nature 1992, 356, 126-131.
4. (c) Wang, Y.; Patel, D. J. Structure 1993, 1, 263-282.
5. (d) Aboul-el, F.; Murchie, A. I. H.; Norman, D. G.; Lilley, D. M. J. J. Mol. Biol. 1994, 243, 458-471.
6. (e) Laughlan, G.; Murchie, A. I. H.; Norman, D. G.; Moore, M. H.; Moody, P. C. E.; Lilley, D. M. J.; Luisi, B. Science 1994, 265, 520-524.
7. (f) Phillips, K.; Dauter, Z.; Murchie, A. I. H.; Lilley, D. M. J.; Luisi, B. J. Mol. Biol. 1997, 273, 171-182.
8. Wellinger, R. J.; Sen, D. Eur. J. Cancer 1997, 33, 735-749.
9. (a) Raymond, E.; Sun, D.; Chen, S.-F.; Windle, B.; Von Hoff, D. D. Curr. Opin. Biotechn. 1996, 7, 583-591.
10. (b) Salazar, M.; Thompson, B. D.; Kerwin, S. M.; Hurley, L. H. Biochemistry 1996, 35, 16110-16115.
11. (c) Perry, P. J.; Kelland, L. R. Expert Opin. Ther. Patents 1998, 8, 1567-1586.
12. (a) Sun, D.; Thompson, B.; Cathers, B. E.; Salazar, M.; Kerwin, S. M.; Trent, J. O.; Jenkins, T. C.; Neidle, S.; Hurley, L. H. J. Med. Chem. 1997, 40, 2113-2116.
13. (b) Perry, P, J.; Gowan, S. M.; Reszka, A. P.; Polucci, P.; Jenkins, T. C.; Kelland, L. R.; Neidle, S. J. Med. Chem. 1998, 41, 3253-3260.
14. (c) Fedoroff, O. Y.; Salazar, M.; Han, H.; Chemeris, V. V.; Kerwin, S. M.; Hurley, L. H. Biochemistry 1998, 37, 12367-12374.
15. (d) Perry, P. J.; Reszka, A. P.; Wood, A. A.; Read, M. A.; Gowan, S. M.; Dosanjh, H. S.; Trent, J. O.; Jenkins, T. C.; Kelland, L. R.; Neidle, S. J. Med. Chem. 1998, 41, 4873-4884.
16. Anantha, N. V.; Azam, M.; Sheardy, R. D. Biochemistry 1998, 37, 2709-2714.
17. Wheelhouse, R. T.; Sun, D.; Han, H.; Han, F. X.; Hurley, L. H. J. Am. Chem. Soc. 1998, 120, 3261-3262.
18. Zahler, A. M.; Williamson, J. R.; Cech, T. R.; Prescott, D. M. Nature 1991, 350, 718-720.
19. (a) Kim, N. W.; Piatyszek, A. M.; Prowse, K. R.; Harley, C. B.; West, M. D.; Ho, P. L. C.; Coviello, G. M.; Wright, W. E.; Weinrich, S. L.; Shay, J. W. Science 1994, 266, 2011-2015.
20. (b) Rhyu, M. S. J. Natl. Cancer Inst. 1995, 87, 884-894.
21. (c) Lundblad, V.; Wright, W. E. Cell 1996, 87, 369-375.
22. (d) Holt, S. E.; Wright, W. E.; Shay, J. W. Eur. J. Cancer 1997, 33, 761-766.
23. (e) Wright, W. E.; Tesmer, V. M.; Huffman, K. E.; Levene, S. D.; Shay, J. W. Genes Dev. 1997, 11, 2801-2809.
24. Chen, Q.; Kuntz, T. D.; Shafer, R. H. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 2635-2639.
25. (a) Guo, Q.; Lu, M.; Marky, L. A.; Kallenbach, N. R. Biochemistry 1992, 31, 2451-2455.
26. (b) Lu, M.; Guo, Q.; Kallenbach, N. R. Biochemistry 1992, 31, 2455-2459.
27. Arthanari, H.; Basu, S.; Kawano, T. L.; Bolton, P. H. Nucleic Acids Res. 1998, 26, 3724-3728.
28. Venitt, S.; Crofton-Sleigh, C.; Agbandje, M.; Jenkins, T. C.; Neidle, S. J. Med. Chem. 1998, 41, 3748-3752.
29. (a) Padmanahhan, K.; Padmanabhan, K. P.; Ferrara, J. D.; Sadler, J. E.; Tulinski, A. J. Biol. Chem. 1993, 268, 17651-17654.
30. (b) Wang, K. Y.; McCurdy, S.; Shea, R. G.; Swaminathan, S.; Bolton, P. H. Biochemistry 1993, 32, 1899-1904.
31. (c) Macaya, R. F.; Schultze, P.; Smith, F. W.; Feigon, J. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 3745-3749.
32. (d) Marathias, V. M.; Wang, K. Y.; Kumar, S.; Pham, T. Q.; Swaminathan, S.; Bolton, P. H. J. Mol. Biol. 1996, 260, 378-394.
33. Jenkins, T. C. In Methods in Molecular Biology, Vol. 90: Drug-DNA Interaction Protocols; Fox, K. R., Ed.; Humana Press: Totawa, 1997; pp 195-218.
34. (a) Cantor, C. R.; Warshaw, M. W.; Shapiro, H. Biopolymers 1970, 9, 1059-1077.
35. (b) Cantor, C. R.; Schimmel, P. R. Biophysical Chemistry, Part III: The Behavior of Biological Macromolecules; W. H. Freeman: New York, 1980; pp 1239-1289.
36. (a) Pastemack, R. F.; Gibbs, E. J.; Villafranca, J. J. Biochemistry 1983, 22, 2406-2414.
37. (b) Pastemack, R. F.; Gibbs, E. J.; Villafranca, J. J. Biochemistry 1983, 22, 5409-5417.
38. (a) Wiseman, T.; Williston, S.; Brandts, J. F.; Lin, L. N. Anal. Biochem. 1989, 179, 131-137.
39. (b) Ladbury, J. E.; Chowdhry, B. Z. Chem. Biol. 1996, 3, 791-801.
40. (c) Haq, I. In Biocalorimetry: Applications of Calorimetry in the Biological Sciences; Ladbury, J. E., Chowdhry, B. Z., Eds.: John Wiley & Sons: Chichester, U.K., 1998; pp 41-61.
41. (a) Job, P. Ann. Chim. (Paris) 1928, 9, 113-203.
42. (b) Likussar, W.; Blotz, D. F. Anal. Chem. 1971, 43, 1265-1272.
43. (c) Huang, C. Y. Methods Enzymol. 1982, 87, 509-525.
44. Pasternack, R. F.; Garrity, P.; Ehrlich, B.; Davis, C. B.; Gibbs, E. J.; Orloff, G.; Giartosio, A.; Turano, C. Nucleic Acids Res. 1986, 14, 5919-5931.
45. Peacocke, A. R.; Skerrett, J. N. H. J. Chem. Soc., Faraday Trans. 1956, 52, 261-279.
46. McGhee, J. D.; von Hippel, P. H. J. Mol. Biol. 1974, 86, 469-489.
47. Cornell, W. D.; Cieplak, P.; Bayly, I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, F.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
48. AMBER parameters for the porphyrin molecule were adapted from Giammona, D. A. Ph.D. Thesis, University of California, Davis, CA, 1984; see http://www.amber.ucsf.edu/amber/ff94/contrib/heme/fremod.hemall.
49. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. J.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. J. Comput. Chem. 1993, 14, 1347-1363.
50. (a) Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269-10280.
51. (b) Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A. J. Am. Chem. Soc. 1993, 115, 9620-9631.
52. Ford, K. G.; Pearl, L. H.; Neidle, S. Nucleic Acids Res. 1987, 15, 6553-6562.
53. -1]. This procedure was used to obtain the models required for further MD simulations, after thermal equilibration at 300 K using H-bonded restraints.
54. (a) Williamson, J. R. Annu. Rev. Biophys. Biomol. Struct. 1994, 23, 703-730.
55. (b) Wyatt, J. R.; Davis, P. W.; Freier, S. M. Biochemistry 1996, 35, 8002-8008.
56. (a) Haq, I.; Ladbury, J. E.; Chowdhry, B. Z.; Jenkins, T. C. J. Am. Chem. Soc. 1996, 118, 10693-10701.
57. (b) Haq, I.; Ladbury, J. E.; Chowdhry, B. Z.; Jenkins T. C.; Chaires, J. B. J. Mol. Biol. 1997, 271, 244-257.
58. (a) Jin, R.; Gaffney, B.L.; Wang, C.; Jones, R. A.; Breslauer, K. J. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 8832-8836.
59. (b) Pilch, D. S.; Plum, G. E.; Breslauer, K. J. Curr. Opin. Struct. Biol. 1995, 5, 334-342.
60. (c) Miura, T.; Benevides, J. M.; Thomas, G. J. J. Mol. Biol. 1995, 248, 233-238.
61. Kano, K.; Minamizono, H.; Kitae, T.; Negi, S. J. Phys. Chem. A 1997, 101, 6118-6124 (and references therein).
62. Ross, W. S.; Hardin, C. C. J. Am. Chem. Soc. 1994, 116, 6070-6080.
63. (a) Lipscomb, L. A.; Zhou, F. X.; Presnell, S. R.; Woo, R. J.; Peek, M. E.; Plaskon, R. R.; Williams, L. D. Biochemistry 1996, 35, 2818-2823.
64. (b) Pasternack, R. F.; Gibbs, E. J. In Metal Ions in Biological Systems; Siegel, A., Sigel, H., Eds.: Marcel Dekker: New York, 1997; pp 367-397.
65. (a) Hopkins, H. P.; Fumero, J.; Wilson, W. D. Biopolymers 1990, 29, 445-459.
66. (b) Chaires, J. B.; Priebe, W.; Graves, D. E.; Burke, T. G. J. Am. Chem. Sac. 1993, 115, 5360-5364.
67. Suh, D.; Chaires, J. B. Bioorg. Med. Chem. 1995, 3, 723-728.