Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry

Biochemistry

Volumn 36, Issue 46, 1997, Pages 13989-14002

  Sich, Christian ^a   Ohlenschläger, Oliver ^a   Ramachandran, Ramadurai ^a   Görlach, Matthias ^a   Brown, Larry R ^a  

^a FRITZ LIPMANN INSTITUTE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; ESCHERICHIA COLI; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN RNA BINDING; RNA SEQUENCE; RNA STRUCTURE;

CARBON ISOTOPES; COMPUTER SIMULATION; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; RNA, RIBOSOMAL, 18S;

EID: 0342601355     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi971207g     Document Type: Article

References (104)

1. Aboul-ela, F., Karn, J., & Varani, G. (1995) J. Mol. Biol. 253, 313-332.
2. Aboul-ela, F., Nikonowicz, E. P., & Pardi, A. (1994) FEBS Lett. 347, 261-264.
3. Allain, F. H. T., & Varani, G. (1995) J. Mol. Biol. 250, 333-353.
4. Allain, F. H. T., Gubser, C. C., Howe, P. W. A., Nagai, K., Neuhaus, D., & Varani, G. (1996) Nature 380, 646-650.
5. Altona, C. (1982) Recl. Trav. Chim. Pays-Bas 101, 413-433.
6. Altona, C., & Sundaralingam, M. (1973) J. Am. Chem. Soc. 95, 2333-2344.
7. Babcock, M. S., Pednault, E. P. D., & Olson, W. K. (1993) J. Biomol. Struct. Dyn. 11, 597-627.
8. Bartels, C., Xia, T. H., Billeter, M., Güntert, P., & Wüthrich, K. (1995) J. Biomol. NMR 6, 1-10.
9. Batey, R. T., Inada, M., Kujawinski, E., Puglisi, J. D., & Williamson, J. R. (1992) Nucleic Acids Res. 20, 4515-4523.
10. Bax. A., Clore, G. M., Driscoll, P. C., Gronenborn, A. M., Ikura, M., & Kay, L. E. (1990) J. Magn. Reson. 87, 620-627.
11. Bodenhausen, G., & Ruben, D. J. (1980) Chem. Phys. Lett. 69, 185-189.
12. Braun. W., & Gō, N. (1985) J. Mol. Biol. 186, 611-626.
13. Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R., & Doudna, J. A. (1996) Science 273, 1678-1685.
14. Cheong, C., Varani, G., & Tinoco, I., Jr. (1990) Nature 346, 680-682.
15. Clore, G. M., Bax, A., Driscoll, P. C., Wingfield, P. T., & Gronenborn, A. M. (1990) Biochemistry 29, 8172-8184.
16. Colvin, R. A., White, S. W., Garcia-Blanco, M. A., & Huffman, D. W. (1993) Biochemistry 32, 1105-1112.
17. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., & Kollman, P. A. (1995) J. Am. Chem. Soc. 117, 5179-5197.
18. Davis, P. W., Thurmes, W., & Tinoco, I., Jr. (1993) Nucleic Acids Res. 21, 537-545.
19. Dickerson, R. E. (1989) Nucleic Acids Res. 17, 1797-1803.
20. Dieckmann, T., & Feigon, J. (1994) Curr. Opin. Struct. Biol. 4, 745-749.
21. Feigon, J., Dieckmann, T., & Smith, F. W. (1996) Chem. Biol. 3, 611-617.
22. Fesik, S. W., Eaton, H. L., Olejniczak, E. T., & Zuiderweg, E. R. P. (1990) J. Am. Chem. Soc. 112, 886-888.
23. Fountain, M. A., Serra, M. J., Krugh, T. R., & Turner, D. H. (1996) Biochemistry 35, 6539-6548.
24. Gorenstein, D. G. (1984) Phosphorus-31 NMR: Principles and Applications, Academic Press, New York.
25. Gregorian, R. S., Jr., & Crothers, D. M. (1995) J. Mol. Biol. 248, 968-984.
26. Griesinger, C., & Eggenberger, U. (1992) J. Magn. Reson. 97, 426-434.
27. Grüne, M., Fürste, J. P., Klussmann, S., Erdmann, V. A., & Brown, L. R. (1996a) Nucleic Acids Res. 24, 2592-2596.
28. Grüne, M., Görlach, M., Soskic, V., Klussmann, S., Bald, R., Fürste, J. P., Erdmann, V. A., & Brown, L. R. (1996b) FEBS Lett. 385, 114-118.
29. Grzesiek, S., & Bax, A. (1993) J. Am. Chem. Soc. 115, 12593-12594.
30. Güntert, P., & Wüthrich, K., (1991) J. Biomol. NMR 1, 447-456.
31. Güntert, P., Braun, W., & Wüthrich, K., (1991) J. Mol. Biol. 217, 517-530.
32. Güntert, P., Dötsch, V., Wider, G., & Wüthrich, K., (1992) J. Biomol. NMR 2, 619-629.
33. Güntert, P. Berndt, K. D., & Wüthrich, K. (1993) J. Biomol. NMR 3, 601-606.
34. Heus, H. A., & Pardi, A. (1991a) J. Am. Chem. Soc. 113, 4360-4361.
35. Heus, H. A., & Pardi, A. (1991b) Science 253, 191-194.
36. Heus, H. A., Wijmenga, S. S., van de Yen, F. J. M., & Hilbers, C. W. (1994) J. Am. Chem. Soc. 116, 4983-4984.
37. Hoffman, D. W., Colvin, R. A., Garcia-Blanco, M. A., & White, S. W. (1993) Biochemistry 32, 1096-1104.
38. Holbrook, S. R. Cheong, C., Tinoco, I., Jr., & Kim, S.-H. (1991) Nature 353, 579-581.
39. Jaeger, J. A., & Tinoco, I., Jr. (1993) Biochemistry 32, 12522-12530.
40. Jardetzky, O., & Roberts, G. C. K. (1981) NMR in Molecular Biology, Academic Press, Inc., Orlando, FL.
41. Jucker, F. M., & Pardi, A. (1995) Biochemistry 34, 14416-14427.
42. Kay, L. E., Ikura, M., & Bax, A. (1990) J. Am. Chem. Soc. 112, 888-889.
43. Koradi, R., Billeter, M., & Wüthrich, K., (1996) J. Mol. Graphics 14, 51-55.
44. Kumar, A., Ernst, R. R., & Wüthrich, K., (1980) Biochem. Biophys. Res. Commun. 95, 1-6.
45. Laing, L. G., & Hall, K. B. (1996) Biochemistry 35, 13586-13596.
46. Lee, C.-H., & Sarma, R. H. (1976) J. Am. Chem. Soc. 98, 3541-3548.
47. Legault, P., Farmer, B. T., II, Mueller, L., & Pardi, A. (1994) J. Am. Chem. Soc. 116, 2203-2204.
48. Legault, P., Jucker, F. M., & Pardi, A. (1995) FEBS Lett. 362, 156-160.
49. Lietzke, S. E., Barnes, C. L., Berglund, J. A., & Kundrot, C. E. (1996) Structure 4, 917-930.
50. Lippens, G., Dhalluin, C., & Wieruszeski, J. M. (1995) J. Biomol. NMR 5, 327-331.
51. Marino, J. P., Prestegard, J. H., & Crothers, D. M. (1994a) J. Am. Chem. Soc. 116, 2205-2206.
52. Marino, J. P., Schwalbe, H., Anklin, C., Bermel, W., Crothers, D. M., & Griesinger, C. (1994b) J. Am. Chem. Soc. 116, 6472-6473.
53. Marino, J. P., Gregorian, R. S., Csankovszki, G., & Crothers, D. M. (1995a) Science 268, 1448-1454.
54. Marino, J. P., Schwalbe, H., Anklin, C., Bermel, W., Crothers, D. M., & Griesinger, C. (1995b) J. Biomol. NMR 5, 87-92.
55. Marino, J. P., Schwalbe, H., Glaser, S. J., & Griesinger, C. (1996) J. Am. Chem. Soc. 118, 4388-4395.
56. Milligan, J. F., Groebe, D. R., Witherell, G. W., & Uhlenbeck, O. C., (1987) Nucleic Acids Res. 15, 8783-8798.
57. Mirmira, S. R., & Tinoco, L. Jr. (1996) Biochemistry 35, 7664-7674.
58. Moore, P. B. (1993) Curr. Opin. Struct. Biol. 3, 340-344.
59. Moore, P. B. (1995) Acc. Chem. Res. 28, 251-256.
60. Mooren, M. M. W., Wijmenga, S. S., van der Marel, G. A., van Boom, J. H., & Hilbers, C. W. (1994) Nucleic Acids Res. 22, 2658-2666.
61. Nikonowicz, E. P., & Pardi, A. (1993) J. Mol. Biol. 232, 1141-1156.
62. Nikonowicz, E. P., Sirr, A., Legault, P., Jucker, F. M., Baer, L. M., & Pardi, A. (1992) Nucleic Acids Res. 20, 4507-4513.
63. Norwood, T. J., Boyd, J., Heritage, J. E., Soffe, N., & Campbell, I. D. (1990) J. Magn. Reson. 87, 488-501.
64. Olsen, H. B., Ludvigsen, S., & Sørensen, O. W. (1993) J. Magn. Reson. A105, 321-322.
65. Orita, M., Nishikawa, F., Shimayama, T., Taira, K., Endo, Y., & Nishikawa, S. (1993) Nucleic Acids Res. 21, 5670-5678.
66. Pardi, A. (1995) Methods Enzymol. 261, 350-380.
67. Pardi, A., & Nikonowicz, E. P. (1992) J. Am. Chem. Soc. 114, 9202-9203.
68. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., III, Ferguson, D. M., G. L. Seibel, U. C. Singh, P. K. Weiner, & Kollman, P. A. (1995) AMBER 4.1, University of California, San Francisco.
69. Pingoud, A., Fliess, A., & Pingoud, V. (1989) in HPLC of Macromolecules (Oliver, R. W. A., Ed.) pp 183-208, IRL Press at Oxford University Press, Oxford, U.K.
70. Plavec, J., & Chattopadhyaya, J. (1995) Tetrahedron Lett. 36, 1949-1952.
71. Pley, H. W., Flaherty, K. M., & McKay, D. B. (1994a) Nature 372, 111-113.
72. Pley, H. W., Flaherty, K. M., & McKay, D. B. (1994b) Nature 372, 68-74.
73. Puglisi, J. D., & Tinoco, I., Jr. (1989) Methods Enzymol. 180, 304-325.
74. Puglisi, J. D., Wyatt, J. R., & Tinoco, I., Jr. (1990) Biochemistry 29, 4215-4226.
75. Ramachandran, R., Sich, C., Grüne, M., Soskic, V., & Brown, L. R. (1996) J. Biomol. NMR 7, 251-255.
76. Ramachandran, R., Sich, C., Ohlenschläger, O., & Brown, L. R. (1997) J. Magn. Reson. 124, 210-213.
77. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer-Verlag, New York.
78. SantaLucia, J., Jr., & Turner, D. H. (1993) Biochemistry 32, 12612-12623.
79. Santoro, J., & King, G. C. (1992) J. Magn. Reson. 97, 202-207.
80. Schmieder, P., Ippel, J. H., van den Elst, H., van der Marel, G. A., van Boom, J. H., Altona, C., & Kessler, H. (1992) Nucleic Acids Res. 20, 4747-4751.
81. Schmitz, U., & James, T. L. (1995) Methods Enzymol. 261, 3-44.
82. Schwalbe, H., Marino, J. P., King, G. C., Wechselberger, R., Bermel, W., & Griesinger, C. (1994) J. Biomol. NMR 4, 631-644.
83. Schwalbe, H., Marino, J. P., Glaser, S. J., & Griesinger, C. (1995) J. Am. Chem. Soc. 117, 7251-7252.
84. Scott, W. G., Murray, J. B., Arnold, J. R. P., Stoddard, B. L., & Klug, A. (1996) Science 274, 2065-2069.
85. Shen, L. X., Cai, Z., & Tinoco, I., Jr. (1995) FASEB J. 9, 1023-1033.
86. Sich, C., Flemming, J., Ramachandran, R., & Brown, L. R. (1996) J. Magn. Reson. B112, 275-281.
87. Sklenar, V., Peterson, R. D., Rejante, M. R., & Feigon, J. (1993) J. Biomol. NMR 3, 721-727.
88. Stein, E. G., Rice, L. M., & Brünger, A. T. (1997) J. Magn. Reson. 124, 154-164.
89. Szewczak, A. A., Moore, P. B., Chang, Y. L., & Wool, I. G. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 9581-9585.
90. Tate, S., Ono, A., & Kainosho, M. (1995) J. Magn. Reson. B106, 89-91.
91. Tuerk, C., Gauss, P., Thermes, C., Groebe, D. R., Gayle, M., Guild, N., Stormo, G., D'Aubenton-Carafa, Y., Uhlenbeck, O. C., Tinoco, I., Jr., Brody, E. N., & Gold, L. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 1364-1368.
92. Uhlenbeck, O. C. (1990) Nature 346, 613-614.
93. Varani, G., & Tinoco, I., Jr. (1991) Q. Rev. Biophys. 24, 479-532.
94. Varani, G., Wimberley, B., & Tinoco, I., Jr. (1989) Biochemistry 28, 7760-7772.
95. Varani, G., Cheong, C., & Tinoco, I., Jr. (1991) Biochemistry 30, 3280-3289.
96. Varani, G., Aboul-ela, F., & Allain, F. H.-T. (1996) Prog. NMR Spectrosc. 29, 51-121.
97. Vister, G. W., & Bax, A. (1992) J. Magn. Reson. 98, 428-435.
98. Vuister, G. W., Wang, A. C., & Bax, A. (1993) J. Am. Chem. Soc. 115, 5334-5335.
99. Woese, C. R., Winkler, S., & Gutell, R. R. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 8467-8471.
100. Wolters, J. (1992) Nucleic Acids Res. 20, 1843-1850.
101. Wu, M., & Turner, D. H. (1996) Biochemistry 35, 9677-9689.
102. Wüthrich, K., (1986) NMR of Proteins and Nucleic Acids, John Wiley & Sons, New York.
103. Wyatt, J. R., Chastain, M., & Puglisi, J. D. (1991) Biotechniques 11, 764-769.
104. Xia, T. (1992) Ph.D. Thesis, ETH-Zürich.