Rational design of anthracene-based DNA binders

Journal of Physical Chemistry B

Volumn 113, Issue 6, 2009, Pages 1710-1721

  Duff Jr , Michael R ^a   Mudhivarthi, Vamsi K ^a   Kumar, Challa V ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTHRACENE; BINDERS; DESIGN; DNA; ENTHALPY; FREE ENERGY; GENES; IONIC STRENGTH; NUCLEIC ACIDS; POLYMERS; PROBES; SODIUM CHLORIDE; TUNING;

ANTHRACENE DERIVATIVES; BINDING ENTHALPIES; BINDING FREE ENERGIES; CONFORMATIONAL CHANGES; CURRENT DATUM; DNA BINDINGS; ENERGY CONTRIBUTIONS; IONIC INTERACTIONS; LINEAR CORRELATIONS; METHYLENE GROUPS; POLYELECTROLYTE EFFECTS; QUANTITATIVE APPROACHES; RATIONAL DESIGNS; SIDE CHAINS; SPECIFIC INTERACTIONS; STRUCTURAL FEATURES; SYSTEMATIC DESIGNS;

BINDING ENERGY;

EID: 61949281323     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp807164f     Document Type: Article

References (75)

1. Molecular Aspects of Anticancer Drug-DNA Interactions; Neidle, S., Waring, M., Eds.; CRC: Boca Raton, FL, 1993.
2. (a) Chaires, J. B. Biopolymers 1997, 44, 201-215.
3. (b) Lane, A. N.; Jenkins, T. C. Q. Rev. Biophys. 2000, 33, 255-306.
4. (c) Graves, D. E; Velea, L. M. Curr. Org. Chem. 2000, 4, 915-929.
5. (d) Haq, I.; Ladbury, J. J. Mol. Recognit. 2000, 13, 188-197.
6. Haq, I.; Jenkins, T. C.; Chowdhry, B. Z.; Ren, J.; Chaires, J. B. Methods Enzymol. 2000, 323, 373-405.
7. (a) Frei, E.; Luce, J. K.; Loo, T. L. Cancer Chemother. Rep., Part 1 1971, 55, 91-97.
8. (b) Wilson, W. L.; Weiss, A. J.; Andrews, N. C. Cancer Chemother. Rep., Part 1 1971, 55, 525.
9. (c) Wunz, T. P.; Dorr, R. T.; Alberts, D. S.; Tunget, C. L-; Einspabr, J.; MiJton, S.; Remers, W. A. J. Med. Chem. 1987, 30, 1313-1321.
10. (a) Renters, W. A.; Wunz, T. P.; Dorr, R. T.; Alberts, D. S.; Tunget, C. L.; Einspahr, J.; Milton, S. J. Med. Chem. 1987, 30, 1313-1321.
11. (b) Wang, L.; Price, H. L.; Jusola, J.; Kline, M; Phanstiel, O., IV. J. Med. Chem. 2001, 44, 3682-3691.
12. (a) Goodsell, D. S.; Kopka, M. L.; Dickerson, R. E. Biochemistry 1995, 34, 4983-4993.
13. (b) Li, Z.; Kim, H. Y.; Tamura, P, J.; Harris, C. M.; Harris, T. M.; Stone, M. P. Biochemistry 1999, 38, 16045-16057.
14. (a) Wilson, W. D.; Wang, Y. H.; Kusuma, S.; Cbandrasekharan, S.; Uang, N. C.; Boykin, D. W. J. Am. Chem. Soc. 1985, 107, 4989-4995.
15. (b) Rodger, A.; Taylor, S.; Adlam, G.; Blagbrough, I. S.; Haworth, I. S. Bioorg. Med. Chem. 1995, 3, 861-872.
16. (c) Becker, H.-C; Norden, B. J. Am. Chem. Soc. 1999, 121, 11947-11952.
17. (d) Becker, H.-C.; Norden, B. J. Am. Chem. Soc. 2000, 122, 8344-8349.
18. (a) Kumar, C. V.; Asuncion, E. H. J. Am. Chem. Soc. 1993, 115, 8547-8553.
19. (b) Kumar, C. V.; Asuncion. E. H.; Tan, W. B. Tetrahedron 2000, 56, 7027-7040.
20. Modukuru, N. K.; Snow, K. J.; Perrin, B. S., Jr.; Bhambhani, A.; Duff, M.; Kumar, C. V. J. Photochem. Photobiol. A 2006, 177, 43-54.
21. Duff, M. R.; Tan, W. B.; Bhambhani, A.; Perrin, B. S., Jr.; Thota, J.; Rodger, A.; Kumar, C. V. J. Phys. Chem. B 2006, 110, 20693-20701.
22. (a) Modukuru, N. K:, Snow, K. J.; Perrin, B. S., Jr.; Thota, J.; Kumar, C. V. J. Phys. Chem. B 2005, 109, 11810-11818.
23. (b) Rodger, A.; Taylor, S.; Adlam, G.; Blagbrough. I. S.; Haworth, I. S. Bioorg. Med. Chem. 1995, 3, 861-872.
24. Tan, W. B.; Bhambhani, A.; Duff, M. R.; Rodger, A.; Kumar, C. V. Photochem. Photobiol. 2006, 82, 20-30.
25. Maniatis, T,; Fritsch, E, F,; Sambrook, J. Molecular Cloning; A Laboratory Manual: Cold Spring Harbor Laboratory. New York, 1982; p 458.
26. (a) Barton, J. K.; Goldberg, J. M.; Kumar, C. V.; Turro, N. J. J. Am. Chem. Soc. 1986, 108, 2081-2088.
27. (b) Baguley, B. C.; Falkenhaug, E. M. Nucleic Acids Res. 1978, 5, 161-171.
28. Nguyen, T.; Francis, M. B. Org. Lett. 2003, 5, 3245-3248.
29. (a) Breslauer, K. J.; Freire, E.; Straume, M. Methods Enzymol. 1992, 231, 533-567.
30. (b) Sturtevant, J. M. Annu. Rev. Biochem. 1987, 38, 463-88.
31. Jelesarov, I.; Bosshard, H. R. J. Mol. Recognit. 1999, 12, 3-18.
32. McGhee, J. D.; von Hippel, P, H. J. Mol. Biol. 1974, 86, 469-489.
33. (a) Scatchard, G. Ann. N.Y. Acad. Sci. 1949, 660-672.
34. (b) Jenkins, T. A. Methods Mol. Biol. 1998, 90, 195-218.
35. (a) Manning, G. S. Q. Rev. Biophys. 1978, 11, 179-246.
36. (b) Record, M. T., Jr.; Anderson, C. F.; Lohman, T. M. Q. Rev. Biophys. 1978, 11, 103-178.
37. (c) Hutchins, R. A.; Crenshaw. J. M.; Graves, D. E.; Denny, W. A. Biochemistry 2003, 42, 13754-13761.
38. Wilson, D. W.; Lopp, I. G. Biopolymers 1979, 18, 3024-3041.
39. Record, M. T., Jr.; Anderson, C. F.; Lohman, T. M. Q. Rev. Biophys. 1978, 11, 103-178.
40. Wunz, T. P.; Craven, M. T.; Karol, M. D.; Hill, G. C.; Renters, W. A. J. Med. Chem. 1990, 33, 1549-1553.
41. Bhambhani, A.; Kumar, C. V. Microporous Mesoporous Mater. 2008, 109, 223-232.
42. Galisteo, M. L.; Mateo, P. L.; Sanchez-Ruiz, J. M. Biochemistry 1991, 30, 2061-2066.
43. (a) Perrin, D. D.; Dempsey, B. Buffers for pH and Metal Ion Control; Chapman and Hall Laboratory Manuals: London, 1974.
44. (b) Bates, R.; Hetzer, H. J. Phys. Chem. 1961, 65, 667-671.
45. (a) Peterson, S. B.; Fojan, P.; Peterson, E. 1.; Peterson, M. T. N. J. Biomed. Biotech. 2001, 1, 62-69.
46. (b) Huang, T.; Pawliszyn, J. Electrophoresis 2002, 23, 3504-3510.
47. Jelesarov, L; Bosshard, H. R. J. Mol. Recognit. 1999, 12, 3-18.
48. (a) Kumar, C. V.; Asuncion, E. H.; Tan, W. B. Tetrahedron 2000, 56, 7027-7040.
49. (b) Modukuru, N. K.; Snow, K. J.; Perrin, B. S., Jr.; Thota, J.; Kumar, C. V. J. Phys. Chem. B 2005, 109, 11810-11818.
50. (c) Modukuru, N. K.; Snow, K, J.; Perrin, B. S., Jr.; Bhambhani, A.; Duff, M.; Kumar, C. V. J. Photochem. Photobiol., A 2006, 177, 43-54.
51. (d) Tan, W. B.; Bhambhani, A.; Duff, M. R.; Rodger, A.; Kumar, C. V. Photochem. Photobiol. 2006, 82, 20-30.
52. Kozurkova, M.; Sabolova, D.; Paulikova, H.; Janovec, L.; Kristian, P.; Bajdichova, M.; Busa, J.; Podhradsky, D.; Imrich, J. Int. J. Biol. Macromol. 2007, 41, 415-422.
53. Lyng, R.; Hard, T.; Norden, B. Biopolymers 1987, 26, 1327-1345.
54. Ardhammar, M.; Norden, B.; Kurucsev, T, DNA-Drug Interactions. In Circular Dichriosm, 2nd ed.; Berova, N., Nakanishi, K., Woody, R. W., Eds.; Wiley-VCH: New York, 2000; pp 741-768.
55. Feigon, J.; Denny, W. A.; Leupin. W.; Kearns, D. R. J, Med. Chem. 1984, 27, 450-465.
56. (a) Baguley, B. G; Denny, W. A.; Atwell, G. J.; Cain, B. F. J. Med. Chem. 1981, 24, 170-177.
57. (b) Morgan, A. R.; Lee, J. S.; Pulleyblank, D. E.; Murray, N. L.; Evans, D. H. Nucleic Acids Res. 1979, 7, 547-569.
58. Graves, D. E.; Velea, L. M. Curr. Org. Chem. 2000, 4, 915-929.
59. Le Pecq, J. B.; Paoletti, C, X Mol. Biol. 1967, 27, 87-106.
60. Culajay, J. F.; Blaber, S. I.; Khurana, A.; Biaber, M. Biochemistry 2000, 59, 7153-7158.
61. Klump, H. In Biochemical Thermodynamics; Jones, M. N., Ed.; Elsevier; Amsterdam, The Netherlands, 1988, p 100.
62. (a) Klump, H. Ber. Bunsen-Ges. Phys. Chem. 1987, 91, 2018.
63. (b) Klump, H.; Hereon, K. Ber. Bunsen-Ges. Phys. Chem. 1984, 88, 20-24.
64. (c) Kurnit, D.; Shark, B.; Maio, J. J. Mol. Biol. 1973, 81, 273-278.
65. Greiner, G.; Maier, I. J. Chem. Soc., Perkin Trans 2 2002, 1005-1011.
66. Shibata, T.; Torigoe, H.; Shibata, Y.; Maeda, M.; Sasaki, S. Nucleic Acids Symp. Ser. 1999, 42, 251-252.
67. Breslauer, K. J.; Remta, D. P.; Chou, W.-Y.; Ferrante, R.; Curry, J.; Zaunczkowski, D.; Snyder, J. G.; Marky, L. A. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 8922-8926.
68. Dougherty, G.; Pilgram, W. J. CRC Crit. Rev. Biochem. 1982, 12, 103-132.
69. (a) Waring, M. J. J. Mol. Biol. 1965, 13, 269-282.
70. (b) Meehan, T.; Gamper, H.; Becker, J. F. J. Biol. Chem. 1982, 257, 10479-10485.
71. Carvlin, M. J.; Datta-Gupta, N.; Fiel, R. J. Biochem. Biophys. Res. Commun. 1982, 108, 66-73.
72. Nishimura, T.; Takeda, Y.; Shimada, N.; Sakurai, K. Chem. Lett. 2007, 36, 388-389.
73. a values at 7.8 ± 0.2 and above (from fluorescence titrations as a function of pH, data not shown), and BODA should have charge of +2 at pH 7.2.
74. Rekharsky, M. V.; Inoue, Y. Chem. Rev. 1998, 98, 1875-1918.
75. Ohtaka, H.; Muzammil, S.; Schon, A.; Velazquez-Campoy, A.: Vega, S.; Freire, E. Int. J. Biochem. Cell Biol. 2004, 36, 1787-1799.