Effect of cytarabine on the NMR structure of a model Okazaki fragment from the SV40 genome

Biochemistry

Volumn 38, Issue 4, 1999, Pages 1166-1175

  Gmeiner, William H ^a   Konerding, David ^b   James, Thomas L ^b  

^a UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTILEUKEMIC AGENT; CYTARABINE; DEOXYCYTIDINE; DNA FRAGMENT; DOUBLE STRANDED DNA; NUCLEOSIDE ANALOG;

ANTINEOPLASTIC ACTIVITY; ARTICLE; DNA REPLICATION; DNA RNA HYBRIDIZATION; DNA STRAND; DRUG EFFECT; MOLECULAR DYNAMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; SIMIAN VIRUS 40; VIRUS GENOME;

ALGORITHMS; BASE SEQUENCE; CYTARABINE; DNA; DNA, VIRAL; GENOME, VIRAL; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; SIMIAN VIRUS 40;

EID: 0033604863     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi981702s     Document Type: Article

References (67)

1. Kelman, Z., Hurwitz, J., and O'Donnell, M. (1998) Structure 6, 121-125.
2. Dutta, A., and Bell, S. P. (1997) Annu. Rev. Cell Dev. Biol. 13, 293-332.
3. Toone, W. M., Aeme, B. L., Morgan, B. A., and Johnston, L. H. (1997) Annu. Rev. Microbiol. 51, 125-149.
4. Broach, J. R., Li, Y. Y., Feldman, J., Jayaram, M., Abraham, J., Nasmyth, K. A., and Hicks, J. B. (1983) Cold Spring Harbor Symp. Quant. Biol. 2, 1165-1173.
5. Foiani, M., Lucchini, G., and Plevani, P. (1997) Trends Biochem. Sci. 22, 424-427.
6. Tomkinson, A. E., and Mackey, Z. B. (1998) Mutat. Res. 407, 1-9.
7. Ogawa, T., and Okazaki, T. (1980) Annu. Rev. Biochem. 49, 421-457.
8. Gilboa, E., Mitra, S. W., Goff, S., and Baltimore, D. (1979) Cell 18, 93-100.
9. Bullock, P. A. (1997) Crit. Rev. Biochem. Mol. Biol. 32, 503-568.
10. Bentley, N. J., and Carr, A. M. (1997) Biol. Chem. 378, 1267-1274.
11. McIntosh, E. M., and Haynes, R. H. (1997) Acta Biochim. Pot. 44, 159-171.
12. Pratt, W. B., Ruddon, R. W., Ensminger, W. D., and Maybaum, J., Eds. (1994) The Anticancer Drugs, 2nd ed., Oxford Press, New York.
13. Caceres-Cortes, J., Sugiyami, H., Ikudome, K., Saito, I., and Wang, A. H.-J. (1997) Eur. J. Biochem. 224, 818-828.
14. Wu, W., Vanderwall, D. E., Lui, S. M., Tang, X., Turner, C. J., Kozarich, J. W., and Stubbe, J. (1996) J. Am. Chem. Soc. 118, 1268-1280.
15. Lown, J. W. (1993) Pharmacol. Ther. 60, 185-214.
16. Gmeiner, W. H. (1998) Curr. Med. Chem. 5, 115-135.
17. Higashigawa, M., Ido, M., Kuwabara, H., Hori, H., Ohkubo, T., Kawasaki, H., Sakurai, M., Taniguchi, K., and Hamazaki, M. (1991) Leuk. Res. 15, 255-262.
18. Johnston, P. G., Takimoto, C. H., Grem, J. L., Fidias, P., Grossbard, M. L., Chabner, B. A., Allegra, C. J., and Chu, E. (1997) Antimetabolites in Cancer Chemotherapy and Biological Response Modifiers 17, pp 1-39, Elsevier, Amsterdam.
19. Gmeiner, W. H., Skradis, A., Pon, R. T., and Liu, J-Q. (1998) Nucleic Acids Res. 26, 2359-2365.
20. Vishwanatha, J. K., Coughlin, S. A., Weselowski-Owen, M., and Baril, E. F. (1986) J. Biol. Chem. 261, 6619-6628.
21. Kufe, D. W., Munroe, D., Herrick, D., Egan, E., and Spriggs, D. (1984) Mol. Pharmacol. 26, 128-134.
22. Ross, D. D., Cuddy, D. P., Cohen, N., and Hensley, D. R. (1992) Cancer Chemother. Pharmacol. 31, 61-70.
23. Selsing, E., Wells, R. D., Early, T. A., and Kearns, D. R. (1978) Nature 254, 249-250.
24. Selsing, E., Wells, R. D., Alden, C. J., and Arnott, S. (1979) J. Biol. Chem. 254, 5417-5422.
25. Selsing, E., and Wells, R. D. (1979) J. Biol. Chem. 254, 5410-5416.
26. Wang, A. H.-J., Satoshi, F., van Boom, J. H., van der Marel, G. A., van Boekel, S. A. A., and Rich, A. (1982) Nature 299, 601-604.
27. Mellema, J.-R., Haasnoot, C. A. G., van der Marel, G. A., Wille, G., van Boekel, C. A. A., van Boom, J. H., and Altoona, C. (1983) Nucleic Acids Res. 11, 5717-5738.
28. Fujii, S., Matsui, S., Tomita, K., Orita, M., Tanaka, T., and Uesugi, S. (1989) Nucleic Acids Symp. Ser. 21, 67-68.
29. Egli, M., Usman, N., Zhang, S., and Rich, A. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 534-538.
30. Salazar, M., Federoff, O. Y., Zhu, L., and Reid, B. R. (1994) J. Mol. Biol. 241, 440-455.
31. Beardsley, G. P., Mikita, T., Klaus, M. M., and Nussbaum, A. L. (1988) Nucleic Acids Res. 16, 9165-9176.
32. States, D. J., Haberkorn, R. A., and Ruben, D. J. (1982) J. Magn. Reson. 48, 286-292.
33. Griesinger, C., Sorenson, O. W., and Ernst, R. R. (1985) J. Am. Chem. Soc. 107, 6394-6396.
34. Borgias, B. A., and James, T. L. (1990) J. Magn. Reson. 87, 475-487.
35. Carper, W. R., and Keller, C. E. (1997) J. Phys. Chem. A 101, 3246-3250.
36. Kim, S.-G., Lin, L.-J., and Reid, B. R. (1992) Biochemistry 31, 3564-3574.
37. Bax, A., and Lerner, L. (1988) J. Magn. Reson. 79, 429-438.
38. Haasnoot, C. A. G., de Leeuw, F. A. A. M., and Altona, C. (1980) Tetrahedron 36, 2783-2792.
39. Altona, C., and Sundaralingham, M. (1972) J. Am. Chem. Soc. 94, 8205-8212.
40. Singh, U. C., Weiner, S. J., and Kollman, P. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 755-759.
41. Sahasrabudhe, P. V., and Gmeiner, W. H. (1997) Biochemistry 36, 5981-5991.
42. Sahasrabudhe, P. V., Pon, R. T., and Gmeiner, W. H. (1996) Biochemistry 35, 13597-13608.
43. Baleja, J. D., Pon, R. T., and Sykes, B. D. (1990) Biochemistry 29, 4828-4839.
44. Mujeeb, A., Kerwin, S. M., Kenyon, G. L., and James, T. L. (1993) Biochemistry 32, 13419-13431.
45. Schmitz, U., Ulyanov, N. B., Kumar, A., and James, T. L. (1993) J. Mol. Biol. 234, 373-389.
46. Lavery, R., and Sklenar, H. (1990) CURVES 3.0. Helical Analysis of Irregular Nucleic Acids, Laboratory of Theoretical Biology, CNRS, Paris.
47. Ravishanker, G., Swaminathan, S., Beveridge, D. L., Lavery, R., and Sklenar, H. (1989) J. Biomol. Struct. Dyn. 6, 669-699.
48. Borgias, B. A., and James, T. L. (1988) J. Magn. Reson. 79, 493-512.
49. Hare, D. R., Wemmer, D. E., Chou, S. H., Drobny, G., and Reid, B. R. (1983) J. Mol. Biol. 171, 319-336.
50. Arnott, S., and Hukins, D. W. L. (1972) Biochem. Biophys. Res. Commun. 47, 1504-1510.
51. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer, New York.
52. Sun, W., and Godson, G. N. (1998) J. Mol. Biol. 276, 689-703.
53. White, S., Szewczyk, J. W., Turner, J. M., Baird, E. E., and Dervan, P. B. (1998) Nature 391, 468-471.
54. Jacobo-Molina, A., Ding, J., Nanni, R. G., Clark, A. D., Jr., Lu, X., Tantillo, C., Williams, R. L., Kamer, G., Ferris, A. L., Clark, P., Hizi, A., Hughes, S. H., and Arnold, E. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 6320-6324.
55. Federoff, O. Y., Salazar, M., and Reid, B. R. (1993) J. Mol. Biol. 233, 509-523.
56. Sun, W., and Godson, G. N. (1998) J. Mol. Biol. 276, 689-703.
57. Luger, K., and Richmond, T. J. (1998) Curr. Opin. Struct. Biol. 8, 33-40.
58. Chwang, A. K., and Sundaralingham, M. (1973) Nature 243, 78-79.
59. Remin, M., Darzynkiewicz, E., Ekiel, I., and Shugar, D. (1976) Biochim. Biophys. Acta 435, 405-416.
60. Teng, M.-K., Liaw, Y.-C., van der Marel, G. A., van Boom, J. H., and Wang, A. H.-J. (1989) Biochemistry 28, 4923-4928.
61. Gao, Y.-G., van der Marel, G. A., van Boom, J. H., and Wang, A. H.-J. (1991) Biochemistry 30, 9922-9931.
62. Pieters, J. M. L., de Vroom, E., van der Marel, G. A., van Boom, J. H., and Altona, C. (1989) Eur. J. Biochem. 184, 415-425.
63. Pieters, J. M. L., de Vroom, E., van der Marel, G. A., van Boom, J. H., Koning, T. M. G., Kaptein, R., and Altona, C. (1990) Biochemistry 29, 788-799.
64. Schweitzer, B. I., Mikita, T., Kellogg, G. W., Gardner, K. H., and Beardsley, G. P. (1994) Biochemistry 33, 11460-11475.
65. Murante, R. S., Henricksen, L. A., and Bambara, R. A. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 2244-2249.
66. Ito, T., Tyler, J. K., and Kadonaga, J. T. (1997) Genes Cells 2, 593-600.
67. Hardman, J. G., and Limbird, L. E. (1996) Goodman & Gilman's The Pharmacological Basis of Therapeutics, 9th ed. McGraw-Hill, New York.