Conformational transitions of an unmodified tRNA: Implications for RNA folding

Biochemistry

Volumn 37, Issue 46, 1998, Pages 16349-16359

  Maglott, Emily J ^a   Deo, Sanmitra S ^a   Przykorska, Anna ^b   Glick, Gary D ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA;

ARTICLE; CONFORMATIONAL TRANSITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROCESSING; PROTEIN SECONDARY STRUCTURE; PROTEIN SYNTHESIS; PROTEIN TERTIARY STRUCTURE; RNA CONFORMATION; SITE DIRECTED MUTAGENESIS; YEAST;

BASE SEQUENCE; BUFFERS; HYDROGEN-ION CONCENTRATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OSMOLAR CONCENTRATION; RNA, FUNGAL; RNA, TRANSFER, PHE; SACCHAROMYCES CEREVISIAE; SODIUM;

EID: 0032542064     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi981722u     Document Type: Article

References (83)

1. Bjork, G. R. (1995) in tRNA Structure, Biosynthesis, and Function (Söll, D., and RajBhandary, U. L., Eds.) pp 165-205, ASM Press, Washington, D.C.
2. Yokoyama, S., and Nishimura, S. (1995) in tRNA Structure, Biosynthesis, and Function (Söll, D., and RajBhandary, U. L., Eds.) pp 207-223, ASM Press, Washington, D.C.
3. Helm, M., Brulé, H., Degoul, F., Cepanec, C., Leroux, J.-P., Giegé, R., and Florentz, C. (1998) Nucleic Acids Res. 26, 1636-1643.
4. Serebrov, V. Yu., Vasilenko, K. S., Kholod, N. S., and Kiselev, L. L. (1997) Mol. Biol. 31, 762-767.
5. Kintanar, A., Yue, D., and Horowitz, J. (1994) Biochimie 76, 1192-1204.
6. Sampson, J. R., and Uhlenbeck, O. C. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 1033-1037.
7. Goodwin, J. T., Stanick, W. A., and Glick, G. D. (1994) J. Org. Chem. 59, 7941-7942.
8. Moor, N. A., Ankilova, V. N., and Lavrik, O. I. (1995) Eur. J. Biochem. 234, 897-902.
9. Avis, J. M., Day, A. G., Garcia, G. A., and Fersht, A. R. (1993) Biochemistry 32, 5312-5320.
10. Peterson, E. T., and Uhlenbeck, O. C. (1992) Biochemistry 31, 10380-10389.
11. Beresten, S., Jahn, M., and Söll, D. (1992) Nucleic Acids Res. 20, 1523-1530.
12. Jahn, M., Rogers, M. J., and Söll, D. (1991) Nature 352, 258-260.
13. Perret, V., Garcia, A., Grosjean, H., Ebel, J. P., Florentz, C., and Giegé, R. (1990) Nature 344, 787-789.
14. Schulman, L. H., and Pelka, H. (1990) Nucleic Acids Res. 18, 285-289.
15. Samuelsson, T., Boren, T., Johansen, T.-I., and Lustig, F. (1988) J. Biol. Chem. 263, 13692-13699.
16. Harrington, K. M., Nazarenko, I. A., Dix, D. B., Thompson, R. C., and Uhlenbeck, O. C. (1993) Biochemistry 32, 7617-7622.
17. Curnow, A. W., Kung, F.-L., Koch, K. A., and Garcia, G. A. (1993) Biochemistry 32, 5239-5246.
18. Han, H., and Dervan, P. B. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 4955-4959.
19. Derrick, W. B., and Horowitz, J. (1993) Nucleic Acids Res. 21, 4948-4953.
20. Behlen, L. S., Sampson, J. R., and Uhlenbeck, O. C. (1992) Nucleic Acids Res. 20, 4055-4059.
21. Behlen, L. S., Sampson, J. R., DiRenzo, A. B., and Uhlenbeck, O. C. (1990) Biochemistry 29, 2515-2523.
22. Perret, V., Garcia, A., Puglisi, J., Grosjean, H., Ebel, J. P., Florentz, C., and Giegé, R. (1990) Biochimie 72, 735-744.
23. Hall, K. B., Sampson, J. R., Uhlenbeck, O. C., and Redfield, A. G. (1989) Biochemistry 28, 5794-5801.
24. Arnez, J. G., and Steitz, T. A. (1994) Biochemistry 33, 7560-7567.
25. Sampson, J. R. (1989) Ph.D. Thesis, University of Colorado, Boulder, CO.
26. Goodwin, J. T., Osborne, S. E., Scholle, E. J., and Glick, G. D. (1996) J. Am. Chem. Soc. 118, 5207-5215.
27. Scaringe, S. A., Francklyn, C., and Usman, N. (1990) Nucleic Acids Res. 18, 5433-5441.
28. Przykorska, A., and Szarkowski, J. W. (1980) Eur. J. Biochem. 108, 285-293.
29. England, T. E., and Uhlenbeck, O. C. (1978) Nature 275, 560-561.
30. Peattie, D. A., and Gilbert W. (1980) Proc. Natl. Acad. Sci. U.S.A. 77, 4679-4682.
31. Zueva, V. S., Mankin, A. S., Bogdanov, A. A., and Baratova, L. A. (1985) Eur. J. Biochem. 146, 679-687.
32. Banerjee, A. R., Jaeger, J. A., and Turner, D. H. (1993) Biochemistry 32, 153-163.
33. Cole, P. E., Yang, S. K., and Crothers, D. M. (1972) Biochemistry 11, 4358-4368.
34. Coutts, S. M., Riesner, D., Römer, R., Rabl, C. R., and Maass, G. (1975) Biophys. Chem. 3, 275-289.
35. Privalov, P. L., and Filimonov, V. V. (1978) J. Mol. Biol. 122, 447-464.
36. Riesner, D., Maass, G., Thiebe, R., Philippsen, P., and Zachau, H. G. (1973) Eur. J. Biochem. 36, 76-88.
37. Urbanke, C., Römer, R., and Maass, G. (1973) Eur. J. Biochem. 33, 511-516.
38. Hinz, H.-J., Filimonov, V. V., and Privalov, P. L. (1977) Eur. J. Biochem. 72, 79-86.
39. Friederich, M. W., and Hagerman, P. J. (1997) Biochemistry 36, 6090-6099.
40. Ehresmann, C., Baudin, F., Mougel, M., Romby, P., Ebel, J.-P., and Ehresmann, B. (1987) Nucleic Acids Res. 15, 9109-9128.
41. Romby, P., Moras, D., Dumas, P., Ebel, J. P., and Giegé, R. (1987) J. Mol. Biol. 195, 193-204.
42. Privalov, P. L., Filimonov, V. V., Venkstern, T. V., and Bayev, A. A. (1975) J. Mol. Biol. 97, 279-288.
43. Gluick, T. C., Gerstner, R. B., and Draper, D. E. (1997) J. Mol. Biol. 270, 451-463.
44. Willick, G. E., and Kay, C. M. (1971) Biochemistry 10, 2216-2222.
45. Guéron, M., and Leroy, J. L. (1982) Biophys. J. 38, 231-236.
46. Leroy, J.-L., Guéron, M., Thomas, G., and Favre, A. (1977) Eur. J. Biochem. 74, 567-574.
47. Leroy, J.-L., and Guéron, M. (1977) Biopolymers 16, 2429-2446
48. Walters, J. A. L. I., Geerdes, H. A. M., and Hilbers, C. W. (1977) Biophys. Chem. 7, 147-151.
49. Plum, G. E., and Breslauer, K. J. (1995) J. Mol. Biol. 248, 679-695.
50. Record, M. T., Jr., Woodbury, C. P., and Lohman, T. M. (1976) Biopolymers 15, 893-915.
51. Przykorska, A., El Adlouni, C., Keith, G., Szarkowski, J. W., and Dirheimer, G. (1992) Nucleic Acids Res. 20, 659-663.
52. Przykorska, A. (1995) Biochimie 77, 109-112.
53. Kan, L. S., Borer, P. N., and Ts'o, P. O. P (1975) Biochemistry 14, 4864-4869.
54. Lockard, R. E., and Kumar, A. (1981) Nucleic Acids Res. 9, 5125-5140.
55. Holbrook, S. R., Sussman, J. L., Warrant, R. W., and Kim, S.-H. (1978) J. Mol. Biol. 123, 631-660.
56. Szewczak, A., and Cech, T. R. (1997) RNA 3, 838-849.
57. Heerschap, A., Mellema, J.-R., Janssen, H. G. J. M., Walters, J A. L. I., Haasnoot, C. A. G., and Hilbers, C. W. (1985) Eur. J. Biochem. 149, 649-655.
58. Hilbers, C. W., Heerschap, A., Haasnoot, C. A. G., and Walters, J. A. L. I. (1983) J. Biomol. Struct. Dyn. 1, 183-207.
59. Li, Z. Q., Giegé, R., Jacrot, B., Oberthür, R., Thierry, J.-C., and Zaccaï, G. (1983) Biochemistry 22, 4380-4388.
60. Aultman, K. S., and Chang, S. H. (1982) Eur. J. Biochem. 124, 471-476.
61. Johnston, P. D., and Redfield, A. G. (1981) Biochemistry 20, 1147-1156.
62. Johnston, P. D., and Redfield, A. G. (1981) Biochemistry 20, 3996-4006.
63. Vlassov, V. V., Giegé, R., and Ebel, J.-P. (1981) Eur. J. Biochem. 119, 51-59.
64. Wrede, P., Wurst, R., Vournakis, J., and Rich, A. (1979) J. Biol. Chem. 254, 9608-9616.
65. Rhodes, D. (1977) Eur. J. Biochem. 81, 91-101.
66. Römer, R., and Hach, R. (1975) Eur. J. Biochem. 55, 271-284.
67. Rhodes, D. (1975) J. Mol. Biol. 94, 449-460.
68. Prinz, H., Maelicke, A., Cramer, F. (1974) Biochemistry 13, 1322-1326.
69. Maglott, E. J., and Glick, G. D. (1997) Nucleic Acids Res. 25, 3297-3301.
70. Draper, D. E. (1992) Acc. Chem. Res. 25, 201-207.
71. Lynch, D. C., and Schimmel, P. R. (1974) Biochemistry 13, 1841-1852.
72. Robison, B., and Zimmerman, T. P. (1971) J. Biol. Chem. 246, 110-117.
73. Hyman, E. S. (1980) Biochim. Biophys. Acta 600, 553-570.
74. Saenger, W. (1984) Principles of Nucleic Acid Structure; pp 331-349, Springer-Verlag, New York.
75. Sprinzl, M., and Gauss, D. H. (1983) in The Modified Nucleosides of Transfer RNA II (Agris, P. F., and Kopper, R. A., Eds.) pp 129-226, Alan R. Liss, Inc., New York.
76. Dirheimer, G., Keith, G., Dumas, P., and Westhof, E. (1995) in tRNA Structure, Biosynthesis, and Function (Söll, D., and RajBhandary, U. L., Eds.) pp 93-126, ASM Press, Washington, D.C.
77. Yue, D., Kintanar, A., and Horowitz, J. (1994) Biochemistry 33, 8905-8911.
78. Pongs, O., and Reinwald, E. (1973) Biochem. Biophys. Res. Commun. 50, 357-363.
79. Cameron, V., and Uhlenbeck, O. C. (1973) Biochem. Biophys. Res. Commun. 50, 635-640.
80. Krzyzosiak, W. J., and Ciesiolka, J. (1983) Nucleic Acids Res. 11, 6913-6921.
81. Davis, D. R., and Poulter, C. D. (1991) Biochemistry 30, 4223-4231.
82. Davanloo, P., Sprinzl, M., Watanabe, K., Albani, M., and Kersten, H. (1979) Nucleic Acids Res. 6, 1571-1581.
83. Horie, N., Hara-Yokoyama, M., Yokoyama, S., Watanabe, K., Kuchino, Y., Nishimura, S., and Miyazawa, T. (1985) Biochemistry 24, 5711-5715.