Solution structure of the aminoacyl-capped oligodeoxyribonucleotide duplex (W-TGCGCAC)2

Biochemistry

Volumn 38, Issue 39, 1999, Pages 12597-12606

  Ho, William C ^a   Steinbeck, Christoph ^a,b   Richert, Clemens ^a  

^a TUFTS UNIVERSITY   (United States)

^b MAX PLANCK INSTITUTE FOR CHEMICAL ECOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; AMINO ACID; DOUBLE STRANDED DNA; INDOLE DERIVATIVE; NUCLEIC ACID BASE; TRYPTOPHAN;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CONFORMATION; CONTROLLED STUDY; DNA PROTEIN COMPLEX; ENTHALPY; ENZYME SUBSTRATE COMPLEX; HYDROGEN BOND; MELTING POINT; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL;

BASE SEQUENCE; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; SOLUTIONS; THERMODYNAMICS; ULTRAVIOLET RAYS;

EID: 0033613177     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi991169w     Document Type: Article

References (69)

1. Olins, D. E., Olins, A. L., and von Hippel, P. H. (1967) J. Mol. biol. 24, 157-176.
2. Werner, M. H., Clore, G. M., Fisher, C. L., Fisher, R. J., Trinh, L., Shiloach, J., and Gronenborn, A. M. (1995) Cell 83, 761-771.
3. Werner, M. H., Clore, G. M., Fisher, C. L., Fisher, R. J., Trinh, L., Shiloach, J., and Gronenborn, A. M. (1996) Cell 87, U23.
4. Werner, M. H., Gronenborn, A. M., and Clore, G. M. (1997) Science 276, 1957.
5. Werner, M. H., Clore, G. M., Fisher, C. L., Fisher, R. J., Trinh, L., Shiloach, J., and Gronenborn, A. M. (1997) J. Biomol. NMR 10, 317-328.
6. Suzuki, M. (1994) Structure 2, 317-326, and references therein.
7. Werner, M. H., Gronenborn, A. M., Clore, G. M. (1996) Science 271, 778-784.
8. Bewley, C. A., Gronenborn, A. M., and Clore, G. M. (1998) Annu. Rev. Biophys. Biomol. Struct. 27, 105-131, and references therein.
9. Rice, P. A., Yang, S. W., Mizuuchi, K., and Nash, H. A. (1996) Cell 87, 1295-1306.
10. Bochkarev, A., Pfuetzner, R. A., Edwards, A. M., and Frappier, L. (1997) Nature 385, 176-181, and references therein.
11. Herron, J. N., He, X. M., Ballard, D. W., Blier, P. R., Pace, P. E., Bothwell, A. L. M., Voss, E. W., and Edmundson, A. B. (1991) Proteins: Struct., Funct., Genet. 11, 159-175.
12. Wuttke, D. S., Foster, M. P., Case, D. A., Gottesfeld, J. M., and Wright, P. E. (1997) J. Mol. Biol. 273, 183-206.
13. Schevitz, R. W., Otwinowski, Z., Joachimiak, A., Lawson, C. L., and Sigler, P. B. (1985) Nature 317, 782-786
14. Evans, P. D., Jaseja, M., Jeeves, M., and Hyde, E. I. (1996) Eur. J. Biochem. 242, 567-575.
15. Russell, W. C., Newman, C., Williamson, D. H. (1975) Nature 255,461-462.
16. Wilson, W. D., Tanious, F. A., Barton, H. J., Strekowski, L., Boykin, D. W., and Jones, R. L. (1989) J. Am. Chem. Soc. 111, 5008-5010.
17. Trotta, E., and Paci, M. (1998) Nucleic Acids Res. 26, 4706-4713.
18. Helene, C., and Dimicoli, J.-L. (1972) FEBS Lett., 26, 6-10.
19. Gabbay, E. J., Adawadkar, P. D., and Wilson, W. D., (1976) Biochemistry 15, 146-151.
20. Gabbay, E. J., Adawadkar, P. D., Kapicak, L., Pearce, S., and Wilson, W. D. (1976) Biochemistry 15, 152-157.
21. Robledo-Luiggi, C., Wilson, W. D., Pares, E., Vera, M., Martinez, C. S., Santiago, D. (1991) Biopolymers 31, 907-917.
22. Rajeswari, M. R. (1996) J. Biomol. Struct. Dyn. 14, 25-30.
23. Rajeswari, M. R., Bose, H. S., Kukreti, S., Gupta, A., Chauhan, V. S., and Roy, K. B. (1992) Biochemistry 31, 6237-6241.
24. Roy, K. B., Kukreti, S., Bose, H. S., Chauhan, V. S., Rajeswari, M. R. (1992) Biochemistry 31, 6241-6245.
25. Suzuki, M. (1990) Nature 344, 562-565.
26. Shine, N. R., James, T. L. (1984) Biochemistry 24, 4333-4341.
27. Sartorius, J., Schneider, H. J. (1995) FEBS Lett. 374, 387-392.
28. Mihara, Y, Doi, M., Inohara, T., Kawamura, M., Hamanaka, N., and Ishida, T. (1997) Biochem. Biophys. Res. Commun. 24, 803-806.
29. Mascotti, D. P., and Lohman, T. M. (1997) Biochemistry 36, 7272-7279.
30. Mascotti, D. P., and Lohman, T. M. (1993) Biochemistry 32, 10568-10579.
31. Padmanabhan, S., Zhang, W. T., Capp, M. W., Anderson, C. F., and Record, M. T. (1997) Biochemistry 36, 5193-5206.
32. Zhang, W., Bond, J. P., Anderson, C. F., Lohman, T. M., and Record, M. T. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 2511-2516.
33. Sarracino, D. A., Steinberg, J. A., Vergo, M. T., Woodworth, G. F., Tetzlaff, C. N., and Richert, C. (1998) Bioorg. Med. Chem. Lett. 8, 2511-2516.
34. Brown, P. E. (1970) Biochim. Biophys. Acta 213, 282-289.
35. Tetzlaff, C. N., Schwope, I., Bleczinski, C. F., Steinberg, J. A., and Richert, C. (1998) Tetrahedron Lett. 39, 4215-4218.
36. Marky, L. A., and Breslauer, K. J. (1987) Biopolymers 26, 1601-1620.
37. Sklenar, V., Piotto, M., Leppik, R., and Saudek, V. (1993) J. Magn. Res. Ser. A 102, 241-245.
38. Kumar, A., Ernst, R. R., and Wüthrich, K. (1980) Biochem. Biophys. Res. Commun. 95, 1-6.
39. Bax, A., and Davis, D. G. (1985) J. Magn. Reson. 65, 355-360.
40. Piantini, U., Sørensen, O. W., and Ernst, R. R. (1982) J. Am. Chem. Soc. 104, 6800-6801.
41. Delsuc, M. A. (1989) in Maximum Entropy and Bayesian Methods (Skilling, J., Ed.) pp 285-290, Kluwer Academic: Dordrecht, The Netherlands.
42. Marion, D., and Wüthrich, K. (1983) Biochem. Biophys. Res. Commun. 113, 967-974.
43. Wijmenga, S. S., Mooren, M. M. W., and Hilbers, C. W. (1993) in NMR of Macromolecules, A Practical Approach (Roberts, G. C. K., Ed.) pp 217-288, Oxford University Press, Oxford, U.K.
44. Calculated with a program written in house, using parameters reported in SantaLucia, J., Allawi, H. T., and Seneviratne, A. (1996) Biochemstry 35, 3555-3562.
45. Vesnaver, G., and Breslauer, K. J. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 3569-3573.
46. Scheek, R. M., Boelens, R., Russo, N., van Boom, J. H., and Kaptein, R. (1984) Biochemistry 23, 1371-1376.
47. Feigon, J., Leupin, W., Denny, W. A., and Kearns, D. R. (1983) Biochemistry 22, 5943-5951.
48. Patel, D. J., Shapiro, L., and Hare, D. (1986) J. Biol. Chem. 261, 1223-1229.
49. Walters, K. J., and Russu, I. M. (1993) Biopolymers 22, 943-951.
50. Davies, D. B. (1978) Prog. NMR-Spectrosc. 12, 135-225.
51. Hare, D. R., Wemmer, D. E., Chou, S.-H., and Drobny, G. (1983) J. Mol. Biol. 171, 319-336.
52. A. T. Brünger (1992) X-PLOR, version 3.1, X-PLOR Manual, Yale University Press, New Haven, CT.
53. Stein, E. G., Rice, L. M., and Brünger, A. T. (1997) J. Magn. Reson., Ser. B 124, 154-164.
54. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer, New York.
55. Boger, D. L., Chen, J. H., and Saionz, K. W. (1996) J. Am. Chem. Soc. 118, 1629-1644.
56. Chen, H. F., and Patel, D. J. (1995) J. Mol. Biol. 246, 164-179.
57. Toulme, J.-J., and Helene, C. (1977) J. Biol. Chem. 252, 244-249.
58. Behmoaras, T., Toulme, J. J., and Helene, C. (1981) Nature 292, 858-859.
59. Choo, Y., and Klug, A. (1997) Curr. Opin. Struct. Biol. 7, 117-125.
60. Mandel-Gutfreund, Y., and Margalit, H. (1998) Nucleic Acids Res. 26, 2306-2312.
61. Mascotti, D. P., and Lohman, T. M. (1992) Biochemistry 31, 8932-8946.
62. Trotta, E., D'Ambrosio, E., Ravagnan, G., and Paci. M. (1996) J. Biol. Chem. 271, 27608-27614.
63. Guckian, K. M., Schweitzer, B. A., Ren, R. X.-F., Sheils, C. J., Paris, P. L., Tahmassebi, D. C., and Kool, E. T. (1996) J. Am. Chem. Soc. 118, 8182-8283.
64. Lohse, P. A., and Szostak, J. W. (1996) Nature 381, 442-444
65. Hager, A. J., Pollard, J. D., and Szostak, J. W. (1996) Chem. Biol. 3, 717-725.
66. Suga, H., Lohse, P. A., and Szostak, J. W. (1998) J. Am. Chem. Soc. 120, 1151-1156.
67. Limmer, S., Hofmann, H. P., Ott, G., and Sprinzl, M. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 6199-6202.
68. Schwope, I., Altman, R. K., Stitelman, D. H., and Richert, C. Unpublished results.
69. Humphrey, W., Dalke, A., and Schulten, K. (1996) J. Mol. Graphics 14, 33-38.