Design, synthesis, and analysis of yeast tRNAPhe analogs possessing intra- and interhelical disulfide cross-links

Journal of the American Chemical Society

Volumn 118, Issue 22, 1996, Pages 5207-5215

  Goodwin, Jay T ^a,b   Osborne, Scott E ^a   Scholle, Emily J ^a   Glick, Gary D ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b PFIZER INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DISULFIDE; TRANSFER RNA;

AMINO ACID SUBSTITUTION; ARTICLE; CROSS LINKING; CRYSTAL STRUCTURE; DYNAMICS; OXIDATION; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN FOLDING; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; RNA SYNTHESIS; SYNTHESIS; YEAST;

EID: 0029952554     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja960091t     Document Type: Article

References (107)

1. For reviews and leading examples, see: (a) Shen, L. X.; Cai, Z.; Tinoco, I., Jr. FASEB J. 1995, 9, 1023-1033.
2. (b) Pyle, A. M.; Green, J. B. Curr. Opin. Struct. Biol. 1995, 5, 303-310.
3. (c) Zarrinkar, P. P.; Williamson, J. R. Science 1994, 265, 918-924.
4. (d) Williamson, J. R. Nature Struct. Biol. 1994, 1, 270-272.
5. (e) Draper, D. E. Acc. Chem. Res. 1992, 25, 201-207.
6. (f) Tinoco, I., Jr.; Puglisi, J. D.; Wyatt, J. R. Nucleic Acids Mol. Biol. 1990, 4, 205-226.
7. (g) Wyatt, J. R.; Puglisi, J. D.; Tinoco, I., Jr. BioEssays 1989, 11, 100-106.
8. (h) Crothers, D. M.; Cole, P. E. Conformational Changes of tRNA. In Transfer RNA; Altman, S., Ed.; MIT Press: Cambridge, MA, 1978; pp 196-247.
9. For example, see: (a) Varani, G.; Cheong, C.; Tinoco, I., Jr. Biochemistry 1991, 30, 3280-3289.
10. (b) Holbrook, S. R.; Cheong, C.; Tinoco, I., Jr.; Kim, S.-H. Nature 1991, 353, 579-581.
11. For representative examples, see: (a) Heilek, G. M.; Marusak, R.; Meares, C. F.; Noller, H. F. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 1113-1116.
12. (b) Vlassov, V. V.; Zuber, G.; Felde, B.; Behr, J.-P.; Giegé, R. Nucleic Acids Res. 1995, 23, 3161-3167.
13. (c) Matsuo, M.; Yokogawa, T.; Nishikawa, K.; Watanabe, K.; Okada, N. J. Biol. Chem. 1995, 270, 10097-10104.
14. (d) Han, H.; Dervan. P. B. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 4955-4959.
15. (e) Burrows, C. J.: Rokita, S. E. Acc. Chem. Res. 1994, 27, 295-301.
16. (f) Cload, S. T.; Richardson, P. L.; Huang, Y.-H.; Schepartz, A. J. Am. Chem. Soc. 1993, 115, 5005-5014.
17. (g) Chow, C. S.; Behlen, L. S.; Uhlenbeck, O. C.; Barton, J. K. Biochemistry 1992, 31, 972-982.
18. (h) Tullius, T. D. Curr. Opin. Struct. Biol. 1991, 1, 428-434.
19. Celander, D. W.; Cech, T. R. Biochemistry 1990, 29, 1355-1361.
20. (J) Chow, C. S.; Barton, J. K. J. Am. Chem. Soc. 1990, 112, 2839-2841.
21. (k) Latham, J. A.; Cech, T. R. Science 1989, 245, 276-282.
22. Murakawa, G. J.: Chen, C. B.; Kuwabara, M. D.; Nierlich, D. P.; Sigman, D. S. Nucleic Acids Res. 1989, 17, 5361-5375.
23. Zuckermann, R. N.; Schultz, P. G. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 1766-1770.
24. (n) Stern, S.; Moazed, D.; Noller, H. F. Methods Enzymol. 1988, 164, 481-489.
25. (o) Ehresmann, C.; Baudin, F.; Mougel, M.; Romby, P.; Ebel, J.-P.; Ehresmann, B. Nucleic Acids Res. 1987, 15, 9109-9128.
26. (p) Romby, P.; Moras, D.; Dumans, P.; Ebel, J. P.; Giegé, R. J. Mol. Biol. 1987, 195, 193-204.
27. (q) Kean, J. M.; White, S. A.; Draper, D. A. Biochemistry 1985, 24, 5062-5070.
28. (r) Holbrook, S. R.; Kim, S.-H. Biopolymers 1983, 22, 1145-1166.
29. For representative examples, see: (a) Agrawal, S.; Iyer, R. P. Curr. Opin. Biotechnol. 1995, 6, 12-19.
30. (b) Agris, P. F.; Malkiewicz, A.; Kraszewski, A.; Everett, K.; Nawrot, B.; Sochacka, E.; Jankowska, J.; Guenther, R. Biochimie 1995, 77, 125-134.
31. Gait, M. J.; Grasby, J. A.; Karn, J.; Mersmann, K.; Pritchard, C. E. Nucleosides Nucleotides 1995, 14, 1133-1144.
32. Nawrot, B.; Malkiewicz, A.; Smith, W. S.; Sierzputowska-Gracz, H.; Agris, P. F. Nucleosides Nucleotides 1995, 14, 143-165.
33. (e) Sproat, B. S. J. Biotechnol. 1995, 41, 221-238.
34. (f) Fu, D.-J.; Rajur, S. B.; McLaughlin, L. W. Biochemistry 1994, 33, 13903-13909.
35. (g) Goodwin, J. T.; Glick, G. D. Tetrahedron Lett. 1994, 35, 1647-1650.
36. (h) Grasby, J. A.; Gait, M. J. Biochimie 1994, 76, 1223-1234.
37. Ng, M. M. P.; Benseler, F.; Tuschl, T.: Eckstein, F. Biochemistry 1994, 33, 12119-12126.
38. (j) Richardson, P. L.; Gross, M. L.; Light-Wahl, K. J.; Smith, R. D.; Schepartz, A. BioMed. Chem. Lett. 1994, 4, 2133-2138.
39. (k) Beaucage, S. L.; Iyer, R. P. Tetrahedron 1993, 49, 6123-6194.
40. Fu, D.-J.; Rajur, S. B.; McLaughlin, L. W. Biochemistry 1993, 32, 10629-10637.
41. (m) Heidenreich, O.; Pieken, W.; Eckstein, F. FASEB J. 1993, 7, 90-95 and references therein.
42. (n) Herschlag, D.; Eckstein, F.; Cech, T. R. Biochemistry 1993, 32, 8299-8311.
43. (o) Herschlag, D.; Eckstein, F.; Cech, T. R. Biochemists 1993, 32, 8312-8321.
44. (p) Sproat, B. S. Curr. Opin. Biotechnol. 1993, 4, 20-28.
45. (q) Tuschl, T.; Ng, M. M. P.; Pieken, W.; Benseler, F.; Eckstein, F. Biochemistry 1993, 32, 11658-11668.
46. (r) Usman, N.; Cedergren R. Trends Biochem. Sci. 1992, 17, 334-339.
47. (s) Williams, D. M.; Pieken, W. A.; Eckstein, F. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 918-921.
48. (t) Green, R.; Szostak, J. W.; Benner, S. A; Rich, A.; Usman, N. Nucleic Acids Res. 1991, 19, 4161-4166.
49. (u) Herschlag, D.; Piccirilli, J. A.; Cech, T. R. Biochemistry 1991, 30, 4844-4854.
50. Pieken, W. A.; Olsen, D. B.; Aurup, H.; Williams, D. M.; Heidenreich, O.; Benseler, F.; Eckstein, F. Nucleic Acids Symp. Ser. 1991, 24, 51-53.
51. (w) Piccirilli, J. A.; Krauch, T.; Moroney, S. E.; Benner, S. A. Nature 1990, 343, 33-37.
52. Talbot, S. J.; Goodman, S.; Bates, S. R. E.; Fishwick, C. W. G.; Stockley, P. G. Nucleic Acids Res. 1990, 18, 3521-3528.
53. (y) Caruthers, M. H. Front. Chem. 1989, 1, 55-61.
54. Phe are present.
55. Holbrook, S. R.; Sussman, J. L.; Warrant, R. W.; Kim, S.-H. J. Mol. Biol. 1978, 123, 631-660.
56. Hall, K. B.; Sampson, J. R.; Uhlenbeck, O. C.; Redfield, A. G. Biochemistry 1989, 28, 5794-5801.
57. Osborne, S. E. Ph.D. Thesis, University of Michigan, 1996, pp 38-79.
58. (a) Wang, H.; Zuiderweg, E. R. P.; Glick, G. D. J. Am. Chem. Soc. 1995, 117, 2981-2991.
59. (b) Cain, R. J.; Zuiderweg, E. R. P.; Glick, G. D. Nucleic Acids Res. 1995, 23, 2153-2160.
60. (c) Wang, H.; Osborne, S. E.; Zuiderweg, E. R. P.; Glick, G. D. J. Am. Chem. Soc. 1994, 116, 5021-5022.
61. Clarke, J.; Fersht, A. R. Biochemistry 1993, 32, 4322-4329 and references therein.
62. (11 Glick, G. D. J. Org. Chem. 1991, 56, 6746-6747.
63. (a) Wünsch, E.; Moroder, L.; Romani, S. Hoppe-Seyler's Z. Physiol. Chem 1982, 363, 1461-1464.
64. (b) Bock, H.; Kroner, J. Chem. Ber. 1966, 99, 2039-2051.
65. Scaringe, S. A.; Francklyn, C.; Usman, N. Nucleic Acids Res. 1990, 18, 5433-5441.
66. Schaller, H.; Weimann, G.; Lerch, B.; Khorana, H. G. J. Am. Chem. Soc. 1963, 85, 3821-3827.
67. Sproat, B. S.: Iribarren, A.; Beijer, B.; Pieles, U.; Lamond, A. I. Nucleosides Nudeotides 1991, 10, 25-36.
68. Dihydroxylation of the C5-C6 double bond is not observed under these conditions.
69. (a) Horn, T.; Urdea, M. S. Tetrahedron Lett. 1986, 27, 4705-4708.
70. (b) Beaucage, S. L.; Caruthers, M. H. Tetrahedron Lett. 1981, 22, 1859-1862.
71. Goodwin, J. T.; Ashton, W. A.; Glick, G. D. J. Org. Chem. 1994, 59, 7941-7943 and references therein.
72. Glick, G. D.; Osborne, S. E.; Knitt, D. S.; Marino, J. P., Jr. J. Am. Chem. Soc. 1992, 114, 5447-5448.
73. Behlen, L. S.; Sampson, J. R.; DiRenzo, A. B.; Uhlenbeck, O. C. Biochemistry 1990, 29, 2515-2523.
74. Parvari, R.; Pecht, I.; Soreq, H. Anal. Biochem. 1983, 133, 450-456.
75. XL was used to verify incorporation of the modified bases and cross-links, respectively. See: (a) Silberklang, M.; Gillum, A. M.; RajBhandary, U. L. Methods Enzymol. 1979, 59, 58-109.
76. (b) Butcher, S. E.; Burke, J. M. J. Mol. Biol. 1994, 244, 52-63.
77. Brown, R. S.; Dewan, J. C.; Klug, A. Biochemistry 1985, 24, 4785-4801.
78. (a) Lipsett, M. N. Cold Spring Harbor Symp. Quant. Biol. 1966, 31, 449-455.
79. (b) Lipsett, M. N. J. Biol. Chem. 1967, 242, 4067-4071.
80. (a) Goodwin, J. T.; Osborne, S. E.; Swanson, P. C.; Glick, G. D. Tetrahedron Lett. 1994, 35, 4527-4530.
81. (b) Gao, H.; Chidambaram, N.; Chen, B. C.; Pelham, D. E.; Patel, R.; Yang, M.; Zhou, L.; Cook, A.; Cohen, J. S. Bioconjugate Chem. 1994, 5, 445-453.
82. (c) Milton, J.; Connolly, B. A.; Nikforov, T. T.; Cosstick, R. J. Chem. Soc., Chem. Commun. 1993, 779-780.
83. (d) Ferentz, A. E.; Keating, T. A.; Verdine, G. L. J. Am. Chem. Soc. 1993, 115, 9006-9014.
84. (e) Erlanson, D. A.; Chen, L.; Verdine, G. L. J. Am. Chem. Soc. 1993, 115, 12583-12584.
85. (f) Ferentz, A. E.; Verdine, G. L. J. Am. Chem. Soc. 1991, 113, 4000-4002.
86. Sigurdsson, S. Th.; Tuschl, T.; Eckstein, F. RNA 1995, 1, 575-583.
87. Allerson, C. R.; Verdine, G. L. Chem. Biol. 1995, 2, 667-675.
88. (a) Fu, D.-J.; Benseler, F.; McLaughlin, L. W. J. Am. Chem. Soc. 1994, 116, 4591-4598.
89. (b) Ma, M. Y.-X.; McCallum, K.; Climie, S. C.; Kuperman, R.; Lin, W. C.; Sumner-Smith, M.; Barret, R. W. Nucleic Acids Res. 1993, 21, 2585-2589.
90. (c) Ma, M. Y.-X.; Reid, L. S.; Climie, S. C.; Lin, W. C.; Kuperman, R.; Sumner-Smith, M.; Barnett, R. W. Biochemistry 1993, 52, 1751-1758.
91. Behlen, L. S.; Sampson, J. R.; Uhlenbeck, O. C. Nucleic Acids Res. 1992, 20, 4055-4059.
92. (a) Woisard, A; Fourrey, J.-L.; Favre, A. J. Mol. Biol. 1994, 239, 366-370.
93. (b) Butcher, S. E.; Burke, J. M. Biochemistry 1994, 33, 992-999.
94. Downs, W. D.; Cech, T. R. Biochemistry 1990, 29, 5605-5613.
95. Favre, A.; Thomas, G. Annu. Rev. Biophys. Bioeng. 1981, 10, 175-200.
96. A notable exception is the use of circular permutation to cross-link various sites; see: Nolan, J. M.; Burke, D. H. Pace, N. R. Science 1993, 261, 762-765.
97. Swanson, P. C.; Glick, G. D. BioMed. Chem. Lett. 1993, 3, 2117-2118.
98. (a) Leehey, M. A.; Squassoni, C. A.; Friederich, M. W.; Mills, J. B.; Hagerman, P. J. Biochemistry 1995, 34, 16235-16239.
99. (b) Duckett, D. R.; Murchie, A. I. H.; Lilley, D. M. J. Cell 1995, 83, 1027-1036.
100. (a) Gohlke, C.; Murchie, A. I. H.; Lilley, D. M. J.; Clegg, R. M. Proc. Natl. Acad Sci. U.S.A. 1994, 91, 11660-11664.
101. (b) Tuschl, T.; Gohlke, C.; Jovin, T. M.; Westhof, E.; Eckstein, F. Science 1994, 266, 785-789.
102. Moore, M. J.; Sharp, P. A. Science 1992, 256, 992-997.
103. (a) Chervitz, S. A.; Lin, C. M.; Falke, J. J. Biochemistry 1995, 34, 9722-9733.
104. (b) Careaga, C. L.; Sutherland, J.; Sabeti, J.; Falke, J. J. Biochemistry 1995, 34, 3048-3055.
105. (c) Careaga, C. L.; Falke, J. J. Biophys. J. 1992, 62, 209-216.
106. (d) Falke, J. J.; Koshland, D. E., Jr. Science 1987, 237, 1596-1600.
107. Blatt, N. B.; Osborne, S. E.; Cain, R. J.; Glick, G. D. Biochimie 1993, 75, 433-441.