Direct observation of aminoglycoside - RNA interactions by surface plasmon resonance

Journal of the American Chemical Society

Volumn 119, Issue 16, 1997, Pages 3641-3648

  Hendrix, Martin ^a   Priestley, E Scott ^a   Joyce, Gerald F ^a   Wong, Chi Huey ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOGLYCOSIDE ANTIBIOTIC AGENT; FRAMYCETIN; MESSENGER RNA; PAROMOMYCIN; REV PROTEIN; ANTIINFECTIVE AGENT; VIRUS RNA;

ARTICLE; BINDING SITE; CIRCULAR DICHROISM; HUMAN IMMUNODEFICIENCY VIRUS 1; IN VITRO STUDY; NUCLEOTIDE SEQUENCE; RNA BINDING; RNA STRUCTURE; ANTIBODY AFFINITY; BIOTINYLATION; CHEMISTRY; ENVELOPE GENE; GENETICS; METABOLISM; PROTEIN BINDING; STRUCTURE ACTIVITY RELATION;

ANTI-BACTERIAL AGENTS; ANTIBODY AFFINITY; BASE SEQUENCE; BINDING SITES; BIOTINYLATION; CHEMISTRY, PHARMACEUTICAL; FRAMYCETIN; GENE PRODUCTS, REV; GENES, ENV; HIV-1; PAROMOMYCIN; PROTEIN BINDING; RNA, MESSENGER; RNA, VIRAL; STRUCTURE-ACTIVITY RELATIONSHIP; REV GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS;

EID: 0030985913     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja964290o     Document Type: Article

References (72)

1. (a) Wilson, W. D.; Ratmeyer, L.; Zhao, M.; Strekowski, L.; Boykin, D. Biochemistry 1993, 32. 4098.
2. (b) McConnaughie. A. W.; Spychala. J.; Zhao, M.; Boykin, D.; Wilson, W. D. J. Med. Chem. 1994, 37. 1063.
3. (c) Zhao, M.; Ratmever, L.; Peloquin, R. G.; Yao, S.; Kumar, A.; Spychala. J.; Boykin, D. w.; Wilson. W. D. Bioorg. Med Chem. 1995, 3, 785.
4. (d) Fernandez-Saiz, M.; Schneider, H.-J.; Sartorius, J.; Wilson, W. D. J. Am. Chem. Soc. 1996, 118, 4739.
5. (a) Zapp, M. L.; Stern, S.; Green, M. R. Cell 1993, 74, 969.
6. (b) Werstuck, G.; Zapp. M. L.; Green, M. R. Chem. Biol. 1996, 3, 129.
7. Mei, H.-Y.; Galan, A. A.; Halim, N. S.; Mack, D. P.; Moreland, D. W.; Sanders, K. B.; Truong, H. N.; Czarnik, A. W. Bioorg. Med. Chem. Lett. 1995, 5, 2755.
8. (a) Zapp, M. L.; Green, M. R. Nature 1989, 342, 714-716.
9. (b) Daiy, T. J.; Cook, K. S.; Gray, G. S.; Maione, T. E.; Rusche, J. R. Nature 1989, 342, 816-819.
10. (a) Malim, M. H.; Hauber, J.; Le, S.-Y.; Maizel, J. V.; Cullen, B. R. Nature 1989, 338, 254-257.
11. (b) Malim, M. H., Cullen, B. R. Mol. Cell. Biol. 1993, 13, 6180-6189.
12. (c) Fischer, U.; Meyer, S.; Teufel, M.; Heckel, C,; Lührmann, R.; Rautmann, G. EMBO J. 1994, 13, 4105-4112
13. Wen, W.; Meinkoth, J. L.; Tsien, R. Y.; Taylor, S. S. Cell 1995, 82, 463.
14. (b) Fischer, U.; Huber, J.; Boelens, W. C.; Mattaj, I. W.; Lührmann, R. Cell 1995, 82, 475.
15. (c) Bogerd, H. P.; Fridell, R. A.; Madore, S.; Cullen, B. R. Cell 1995, 82, 485.
16. (d) Stutz, F.; Neville, M.; Rosbach, M. Cell 1995, 82, 495.
17. Park, W. K. C.; Auer, M.; Jaksche, H.; Wong, C.-H. J. Am. Chem. Soc. 1996, 118, 10150.
18. Revzin, A. BioTechniques 1989, 7, 346.
19. (a) Clore, G. M.; Gronenborn, A. M.; Davies, R. W. J. Mol. Biol. 1982, 155, 447.
20. (b) Woodbury, C. P., Jr.; von Hippel, P. H. J. Am. Chem. Soc. 1983, 22, 4730.
21. Malmquist, M. Nature 1993, 361, 186.
22. (a) Heaphy, S.; Dingwall, C.; Ernberg, I.; Gait, M. J.; Green, S. M.; Karm, J.; Lowe, A. D.; Singh, M.; Skinner, M. A. Cell 1990, 60, 685-693.
23. (b) Malim, M. H.; Tiley, L. S.; McCarn, D. F.; Rusche, J. R.; Hauber, J.; Cullen, B. R. Cell 1990, 60, 675-683.
24. (c) Olsen, H. S.; Nelbock, P.; Cochrane, A. W.; Rosen, C. A. Science 1990, 247. 845-848.
25. (d) Holland, S. M.; Ahmad, N.; Maitra, R. K.; Wingfield, P.; Venkatesan, S. J. Virol. 1990, 64, 5966-5975.
26. (e) Heaphy, S.; Finch, J. T.; Gait, M. J.; Karn, J.; Singh, M. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 7366-7370.
27. (f) Kjems, J.; Brown, M.; Chang, D. D.; Sharp, P. A. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 683-687.
28. Peterson, R. D.; Bartel, D. P.; Szostak, J. W.; Horvath, S., J.; Feigon, J. Biochemistry 1994, 33, 5357.
29. (a) Bartel, D. P.; Zapp, M. L.; Green, M. R.; Szostak, J. W. Cell 1991, 67, 529-536.
30. (b) Cook, K. S.; Fisk, G. J.; Hauber, J.; Usman, N.; Daly, T. J.; Rusche, J. R. Nucleic Acids Res. 1991, 19, 1577-1582.
31. (c) Iwai, S.; Pritchard, C.; Mann, D. A.; Karn, J.; Gait, M. J. Nucleic Acids Res. 1992, 24, 6465-6472.
32. Battiste, J. L.; Mao, H.; Rao, N. S.; Tan, R.; Muhandiram, D. R.; Kay, L. E.; Frankel, A. D.; Williamson, J. R. Science 1996, 273, 1547-1551.
33. (a) Wallis, M. G.; von Ahsen, U.; Schroeder, R.; Famulok, M. Chem. Biol. 1995, 2, 543.
34. (b) Famulok, M.; Hüttenhofer, A. Biochemistry 1996, 35, 4265.
35. (a) Mulligan, J. F.; Groebe, D. R.; Witherell, G. W.; Uhlenbeck, O. C. Nucleic Acids Res. 1987, 15, 8783.
36. (b) Milligan, J. F.; Uhlenbeck, O. C. Methods Enzymol. 1989, 180, 51.
37. (a) Malim, M. H.; Böhnlein, S.; Hauber, J.; Cullen, B. R. Cell 1989, 58, 205-214.
38. (b) Malim, M. H.; Cullen, B. R. Cell 1991, 65, 241-248.
39. (c) Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 7734-7738.
40. (a) Battiste, J. L.; Tan, R.; Frankel, A. D.; Williamson, J. R. Biochemistry 1994, 33, 2741.
41. (b) Tan, R.; Chen, L.; Buettner, J. A.; Hudson, D.; Frankel, A. D. Cell 1993, 73, 1031.
42. (c) Kjems, J.; Calnan, B. J.; Frankel, A. D.; Sharp, P. A. EMBO J. 1992, 11, 1119.
43. Surface transport limitations have two important consequences: (1) at low concentration equilibrium cannot be reached during the length of the association phase which makes equilibrium measurements impossible and (2) kinetic measurements are not possible because the observed rates are not interaction controlled.
44. Defined here as the ratio of specific to nonspecific binding when 1 equiv is bound specifically.
45. Chen, Y.-H.; Yang, J. T.; Chau, K. H. Biochemistry 1974, 13, 3350.
46. (a) Wang, Y.; Rando, R. R. Chem Biol. 1995, 2, 281.
47. (b) Lato, S. M.; Boles, A. R.; Ellington, A. D. Chem. Biol. 1995, 2, 291.
48. (c) Wang, Y.; Killian, J.; Hamasaki, K.; Rando, R. R. Biochemistry 1996, 35, 12338.
49. Hendrix, M.; Alper, P. B.; Priestley, E. S.; Wang, C.-H. Angew. Chem., Int. Ed. Engl. 1997, 36, 95.
50. (a) Amils, R.; Ramirez, L.; Sanz, J. L.; Marín, I.; Pisabarro, G.; Ureña, D. Can. J. Microbiol. 1989, 35, 141.
51. (b) Marín, I.; Abad, J. P.; Ureña, D.; Amils, R. Biochemistry 1995, 34, 16519.
52. (a) Tanaka, N. Mechanism of Action of Aminoglycoside Antibiotics. Handbook of Experimental Pharmacology; Springer-Verlag: New York, 1982; Vol. 62, p 221.
53. (b) Cundliffe, E. Recognition Sites for Antibiotics within rRNA. In The Ribosome; Hill, W. E., et al, Eds.; 1990; p 479.
54. (c) Noller, H. F. Annu. Rev. Biochem. 1991, 60, 191.
55. (a) Moazed, D.; Noller, H. F. Nature 1987, 327, 389.
56. (b) Puhroit, P.; Stern, S. Nature 1994, 370, 659.
57. (c) Recht, M. I.; Fourmy, D.; Blanchard, S. C.; Dahlquist, K. D.; Puglisi, J. D. J Mol. Biol. 1996, 202, 421.
58. (d) Miyaguchi, H.; Narita, H.; Sakamoto, K.; Yokoyama, S. Nucleic Acids Res. 1996, 24, 3700.
59. Davies, J.; Davis, B. D. J. Biol. Chem. 1968, 243, 3312.
60. Fourmy, D.; Recht, M. I.; Blanchard, S. C.; Puglisi, J. D. Science 1996, 274, 1367.
61. (a) von Ahsen, U.; Davies, J.; Schroeder, R. Nature 1991, 353, 368.
62. (b) von Ahsen, U.; Davies, J.; Schroeder, R. J. Mol. Biol. 1992, 226, 935.
63. (c) von Ahsen, U.; Noller, H. F. Science 1993, 260, 1500.
64. (a) Stage, T. K.; Hertel, K. J.; Uhlenbeck, O. C. RNA 1995, 1, 95.
65. (b) Clouet-d'Orval, B.; Stage, T. K.; Uhlenbeck, O. C. Biochemistry 1995, 34, 11186.
66. (a) Davies, J. J Mol. Microbiol. 1990, 4, 1227.
67. (b) Davies, J.; von Ahsen, U.; Schroeder, R. In The RNA World; Gesteland, R. F., Atkins, J. F., Eds.; Cold Spring Harbor Laboratory Press: New York, 1993, p 185.
68. (c) Schroeder, R.; Streicher, B.; Wank, H. Science 1993, 260, 1443.
69. (d) Hirao, I.; Ellington, A. D. Curr. Biol. 1995, 5, 1017.
70. LeGoffic, F.; Capmau, M.-L.; Tangy, F.; Baillarge, M. Eur. J. Biochem. 1979, 102, 73.
71. BIAtechnology Handbook; Pharmacia Biosensor AB: Uppsala, 1994; Chapter 4.
72. Umezawa, H.; Kondo, S. Methods Enzymol. 1975, 43, 263.