Solution conformation of an abasic DNA undecamer duplex d(CGCACXCACGC)·d(GCGTGTGTGCG): The unpaired trymine stacks inside the helix

Biochemistry

Volumn 36, Issue 16, 1997, Pages 4817-4830

  Coppel, Yannick ^a   Berthet, Nathalie ^a   Coulombeau, Christian ^a   Coulombeau, Christiane ^a   Garcia, Julian ^a   Lhomme, Jean ^a  

^a UNIVERSITÉ JOSEPH FOURIER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

THYMINE DERIVATIVE;

ARTICLE; DNA CONFORMATION; DNA DETERMINATION; DNA STRUCTURE; HYDROGEN BOND; MOLECULAR DYNAMICS; NUCLEAR OVERHAUSER EFFECT; PHOSPHORUS NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTON NUCLEAR MAGNETIC RESONANCE;

DNA; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; SOFTWARE; THYMINE;

EID: 0030964066     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi962677y     Document Type: Article

References (70)

1. Altona, C., & Sundaralingam, M. (1972) J. Am. Chem. Soc. 94, 8205-8211.
2. Arnott, S., Chandrasekaran, R., Birdsall, D. L., Leslie, A. G. W., & Ratliff, R. L. (1980) Nature (London) 283, 743-745.
3. Bailly, V., & Verly, W. (1989) Nucleic Acids Res. 17, 3617-3618.
4. Baleja, J. D., Pon, R. T., & Sykes, B. D. (1990) Biochemistry 29, 4828-4839.
5. Belmont, P., Boudali, A., Constant, J.-F., Demeunynck, M., Fkyerat, A., Lhomme, J., Michon, P., & Serratrice, G. (1997) New J. Chem. 21, 47-54.
6. Berthet, N. (1995) Ph.D. Thesis, University Joseph Fourier Grenoble I, Grenoble, France.
7. Berthet, N., Boudali, A., Constant, J.-F., Decout, J.-L., Demeunynck, M., Fkyerat, A., Garcia, J., Laayoun, A., Michon, P., & Lhomme, J. (1994) J. Mol. Recognit. 7, 99-107.
8. Boiteux, S., & Laval, J. (1982) Biochemistry 21, 6746-6751.
9. Borgias, B. A., & James, T. L. (1989) Methods Enzymol. 176, 169-183.
10. Borsias, B. A., & James, T. L. (1990) J. Magn. Reson. 87, 475-487.
11. Cai, H., Loom, B., Eritja, R., & Goodman, M. F. (1993) J. Biol. Chem. 268, 23567-23572.
12. Chary, K. V. R., & Modi, S. (1988) FEBS Lett. 233, 319-324.
13. Constant, J.-F., O'Connor, T., Lhomme, J., & Laval, J. (1988) Nucleic Acids Res. 16, 2691-2703.
14. Constant, J.-F., Fkyerat, A., Demeunynck, M., Laval, J., O'Connor, T. R., & Lhomme, J. (1990) Anti-Cancer Drug Des. 5, 59-62.
15. Cuniasse, Ph., Sowers, L. C., Eritja, R., Kaplan, B., Goodman, M. F., Cognet, J. A. H., Lebret, M., Guschlbauer, W., & Fazakerley, G. V. (1987) Nucleic Acids Res. 15, 8003-8022.
16. Cuniasse, Ph., Fazakerley, G. V., Guschlbauer, W., Kaplan, B., & Sowers, L. C. (1990) J. Mol. Biol. 213, 303-314.
17. Demple, B., & Harrison, L. (1994) Annu. Rev. Biochem. 63, 915-948.
18. Feigon, J., Leupin, W., Denny, W. A., & Kearns, D. R. (1983) Biochemistry 22, 5943-5951.
19. Fkyerat, A., Demeunynck, M., Constant, J.-F., Michon, P., & Lhomme, J. (1993a) J. Am. Chem. Soc. 115, 9952-9959.
20. Fkyerat, A., Demeunynck, M., Constant, J.-F., & Lhomme, J. (1993b) Tetrahedron 49, 11237-11252.
21. Fouilloux, L., Berthet, N., Coulombeau, C., Coulombeau, Ce., Dheu-Andries, M.-L., Garcia, J., Lhomme, J., & Vatton, P. (1995) J. Mol. Struct. 330, 417-422.
22. Freeman, R., Friedrich, J., & Xi-Li, W. (1988) J. Magn. Reson. 79, 561-567.
23. Goljer, I., Kumar, S., & Bolton, P. H. (1995) J. Biol. Chem. 270, 22980-22987.
24. Gorenstein, D. G. (1994) Chem. Rev. 94, 1315-1338.
25. Hosur, R. V., Ravikumar, M., Chary, K. V. R., Shteth, A., Govil, G., Zun-Kun, T., & Miles, H. T. (1986) FEBS Lett. 205, 71-76.
26. James, T. L. (1991) Curr. Opin. Struct. Biol. 1, 1042-1053.
27. Kalnick, M. W., Chang, C. N., Grollman, A. P., & Patel, D. J. (1988) Biochemistry 27, 924-931.
28. Kalnick, M. W., Chang, C. N., Johnson, F., Grollman, A. P., & Patel, D. J. (1989a) Biochemistry 28, 3373-3383.
29. Kalnick, M. W., Norman, D. G., Swarm, P. F., & Patel, D. J. (1989b) J. Biol. Chem. 264, 3702-3712.
30. Kalnick, M. W., Norman, D. G., Zagorski, M. G., Swann, P. F., & Patel, D. J. (1989c) Biochemistry 28, 294-303.
31. Kalnick, M. W., Norman, D. G., Li, B. F., Swann, P. F., & Patel, D. J. (1990) J. Biol. Chem. 265, 636-647.
32. Keepers, J. W., & James, T. L. (1984) J. Magn. Reson. 57, 404-426.
33. Lavery, R. (1988) in Structure and Expression; Vol 3, DNA Bending and Curvature (Olson, W. K., Sarma, R. H., Sarma, M. H., & Sundaralingham, M., Eds.) pp 191-211, Adenine Press, New York.
34. Lavery, R., & Sklenar, H. (1988) J. Biomol. Struct. Dyn. 6, 63-91.
35. Lavery, R., & Sklenar, H. (1989) J. Biomol. Struct. Dyn. 6, 655-667.
36. Lavery, R., & Sklenar, H. (1990) CURVES 3.0, Helical Analysis of Irregular Nucleic Acids, Laboratory for Theoretical Biochemistry, CNRS, Paris.
37. Lilley, D. M. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 7140-7142.
38. Lindahl, T. (1993) Nature (London) 362, 709-715.
39. Lindahl, T., & Nyberg, B. (1972) Biochemistry 11, 3610-3618.
40. Liu, H., Thomas, P. D., & James, T. L. (1992) J. Magn. Reson. 98, 163-175.
41. Loeb, L., & Preston, B. (1986) Annu. Rev. Genet. 20, 201-230.
42. Manoharan, M., Ransom, S. C., Mazumder, A., Gerlt, J. A., Wilde, J. A., Withka, J. M., & Bolton, P. H. (1988a) J. Am. Chem. Soc. 110, 1620-1622.
43. Manoharan, M., Mazumder, A., Ransom, S. C., Gerlt, J. A., & Bolton, P. H. (1988b) J. Am. Chem. Soc. 110, 2690-2691.
44. Mazunder, A., Gerlt, J. A., Absalon, M. J., Stubbe, J., Cunnigham, R. P., Withka, J., & Bolton, P. H. (1991) Biochemistry 30, 1119-1126.
45. Metzler, W. J., Wang, C., Kitchen, D. B., Levy, R. M., & Pardi, A. (1990) J. Mol. Biol. 214, 711-736.
46. Miaskiewicz, K., Osman, R., & Weinstein, H. (1993) J. Am. Chem. Soc. 115, 1526-1537.
47. Millican, T. A., Mock, G. A., Chauncey, M. A., Patel, T. P., Eaton, M. A., Gunning, J., Cutbush, S. D., Neidele, S., & Mann, J. (1984) Nucleic Acids Res. 12, 7435-7453.
48. Morden, K. M., Chu, Y. G., Martin, F. G., & Tinoco, I. J. (1983) Biochemistry 22, 5557-5563.
49. Patel, D. J., Kozlowski, S. A., Marky, L. A., Rice, J. A., Broka, C., Itakura, K., & Breslauer, K. J. (1982) Biochemistry 21, 445-451.
50. Plateau, P., & Gueron, M. (1982) J. Am. Chem. Soc. 104, 7310-7311.
51. Poncin, M., Hartmann, B., & Lavery, R. (1992) J. Mol. Biol. 226, 775-794.
52. Randall, S. K., Eritja, R., Kaplan, B., Petruska, J., & Goodman, M. F. (1987) J. Biol. Chem. 262, 6864-6870.
53. Reid, B. R., Banks, K., Flynn, P., & Nerdal, W. (1989) Biochemistry 28, 10001-10007.
54. Rinkel, J. L., & Altona, C. (1987) J. Biomol. Struct. Dyn. 4, 621-649.
55. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer-Verlag, New York.
56. Scheck, R. M., Russo, N., Boelens, R., Kaptein, R., & Van Boom, J. H. (1983) J. Am. Chem. Soc. 105, 2914-2916.
57. Schmitz, U., Pearlman, D. A., & James, T. L. (1991) J. Mol. Biol. 221, 271-292.
58. Singh, M. P., Hill, G. C., Péoc'h, D., Rayner, B., Imbach, J.-L., & Lown, J. W. (1994) Biochemistry 33, 10271-10285.
59. States, D. J., Haberkorn, R. A., & Ruben, D. J. (1982) J. Magn. Reson. 48, 286-292.
60. Takeshita, M., Chang, C.-N., Johnson, F., Will, S., & Grollman, A. P. (1987) J. Biol. Chem. 262, 10171-10179.
61. Taylor, R., Kennard, O., & Versichel, W. (1984) J. Am. Chem. Soc. 106, 244-248.
62. van den Hoogen, Y. T., van Beuzekom, A. A., van den Elst, H., van der Marel, G. A., van Boom, J. H. & Altona, C. (1988) Nucleic Acids Res. 16, 2971-2986.
63. Wallace, S. S. (1988) Environ. Mol. Mutagen. 12, 431-477.
64. Wang, Y., & Patel, D. J. (1994) J. Mol. Biol. 242, 508-526.
65. Weiner, S. J., Kollman, P. A., Nguyen, D. T., & Case, D. A. (1986) J. Comput. Chem. 7, 230-252.
66. Weiss, B., & Grossman, L. (1987) Adv. Enzymol. Relat. Areas Mol. Biol. 60, 1-34.
67. Wilde, J. A., Bolton, P. H., Mazumder, A., Manoharan, M., & Gerlt, J. A. (1989) J. Am. Chem. Soc. 111, 1894-1896.
68. Withka, J. M., Wilde, J. A., & Bolton, P. H. (1991) Biochemistry 30, 9931-9940.
69. Woodson, S. A., & Crothers, D. M. (1988) Biochemistry 27, 8904-8914.
70. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, pp 203-255, John Wiley & Sons, New-York.