Differential binding of Mg2+, Zn2+, and Cd 2+ at two sites in a hammerhead ribozyme motif, determined by 15N NMR

Journal of the American Chemical Society

Volumn 126, Issue 29, 2004, Pages 8908-8909

  Wang, Gang ^a   Gaffney, Barbara L ^a   Jones, Roger A ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CADMIUM; MAGNESIUM ION; RIBOZYME; RNA; ZINC ION; DIVALENT CATION; HAMMERHEAD RIBOZYME; MAGNESIUM; METAL; NITROGEN; ZINC;

ARTICLE; BINDING AFFINITY; BINDING SITE; CRYSTAL STRUCTURE; GEOMETRY; HYDROGEN BOND; METAL BINDING; NITROGEN NUCLEAR MAGNETIC RESONANCE; PROTEIN MOTIF; PROTEIN STRUCTURE; RNA STRUCTURE; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY; CHEMISTRY; METABOLISM; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE;

BINDING SITES; CADMIUM; CATIONS, DIVALENT; MAGNESIUM; METALS; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; RNA, CATALYTIC; ZINC;

EID: 3242762940     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja049804v     Document Type: Article

References (43)

1. Doherty, E. A.; Doudna, J. A. Annu. Rev. Biochem. 2000, 69, 597-615; Eckstein, F.; Bramlage, B. Biopolymers (NAS) 1999, 52, 147-154; DeRose, V. J. Chem. Biol. 2002, 9, 961-969; Takagi, Y.; Warashina, M.; Stec, W. J.; Yoshinari, K.; Taira, K. Nucleic Acids Res. 2001, 29, 1815-1834.
2. Doherty, E. A.; Doudna, J. A. Annu. Rev. Biochem. 2000, 69, 597-615; Eckstein, F.; Bramlage, B. Biopolymers (NAS) 1999, 52, 147-154; DeRose, V. J. Chem. Biol. 2002, 9, 961-969; Takagi, Y.; Warashina, M.; Stec, W. J.; Yoshinari, K.; Taira, K. Nucleic Acids Res. 2001, 29, 1815-1834.
3. Doherty, E. A.; Doudna, J. A. Annu. Rev. Biochem. 2000, 69, 597-615; Eckstein, F.; Bramlage, B. Biopolymers (NAS) 1999, 52, 147-154; DeRose, V. J. Chem. Biol. 2002, 9, 961-969; Takagi, Y.; Warashina, M.; Stec, W. J.; Yoshinari, K.; Taira, K. Nucleic Acids Res. 2001, 29, 1815-1834.
4. Doherty, E. A.; Doudna, J. A. Annu. Rev. Biochem. 2000, 69, 597-615; Eckstein, F.; Bramlage, B. Biopolymers (NAS) 1999, 52, 147-154; DeRose, V. J. Chem. Biol. 2002, 9, 961-969; Takagi, Y.; Warashina, M.; Stec, W. J.; Yoshinari, K.; Taira, K. Nucleic Acids Res. 2001, 29, 1815-1834.
5. McKay, D. B. RNA 1996, 2, 395-403.
6. Pley, H. W.; Flaherty, K. M.; McKay, D. B. Nature (London) 1994, 372, 68-74; Scott, W. G.; Finch, J. T.; Klug, A. Cell 1995, 81, 991-1002; Scott, W. G.; Murray, J. B.; Arnold, J. R. P.; Stoddard, B. L.; Klug, A. Science 1996, 274, 2065-2069; Murray, J. B.; Terwey, D. P.; Maloney, L.; Karpeisky, A.; Usman, N.; Beigelman, L.; Scott, W. G. Cell 1998, 92, 665-673.
7. Pley, H. W.; Flaherty, K. M.; McKay, D. B. Nature (London) 1994, 372, 68-74; Scott, W. G.; Finch, J. T.; Klug, A. Cell 1995, 81, 991-1002; Scott, W. G.; Murray, J. B.; Arnold, J. R. P.; Stoddard, B. L.; Klug, A. Science 1996, 274, 2065-2069; Murray, J. B.; Terwey, D. P.; Maloney, L.; Karpeisky, A.; Usman, N.; Beigelman, L.; Scott, W. G. Cell 1998, 92, 665-673.
8. Pley, H. W.; Flaherty, K. M.; McKay, D. B. Nature (London) 1994, 372, 68-74; Scott, W. G.; Finch, J. T.; Klug, A. Cell 1995, 81, 991-1002; Scott, W. G.; Murray, J. B.; Arnold, J. R. P.; Stoddard, B. L.; Klug, A. Science 1996, 274, 2065-2069; Murray, J. B.; Terwey, D. P.; Maloney, L.; Karpeisky, A.; Usman, N.; Beigelman, L.; Scott, W. G. Cell 1998, 92, 665-673.
9. Pley, H. W.; Flaherty, K. M.; McKay, D. B. Nature (London) 1994, 372, 68-74; Scott, W. G.; Finch, J. T.; Klug, A. Cell 1995, 81, 991-1002; Scott, W. G.; Murray, J. B.; Arnold, J. R. P.; Stoddard, B. L.; Klug, A. Science 1996, 274, 2065-2069; Murray, J. B.; Terwey, D. P.; Maloney, L.; Karpeisky, A.; Usman, N.; Beigelman, L.; Scott, W. G. Cell 1998, 92, 665-673.
10. Rueda, D.; Wick, K.; McDowell, S. E.; Walter, N. G. Biochemistry 2003, 42, 9924-9936; Stage-Zimmermann, T. K.; Uhlenbeck, O. C. Nat. Struct. Biol. 2001, 8, 863-867; Curtis, E. A.; Bartel, D. P. RNA 2001, 7, 546-552; Hammann, C.; Cooper, A.; Lilley, D. M. J. Biochemistry 2001, 40, 1423-1429; Borda, E. J.; Markley, J. C.; Sigurdsson, S. T. Nucleic Acids Res. 2003, 31, 2595-2600; Hampel, K. J.; Burke, J. M. Biochemistry 2003, 42, 4421-4429; Bondensgaard, K.; Mollova, E. T.; Pardi, A. Biochemistry 2002, 41, 11532-11542.
11. Rueda, D.; Wick, K.; McDowell, S. E.; Walter, N. G. Biochemistry 2003, 42, 9924-9936; Stage-Zimmermann, T. K.; Uhlenbeck, O. C. Nat. Struct. Biol. 2001, 8, 863-867; Curtis, E. A.; Bartel, D. P. RNA 2001, 7, 546-552; Hammann, C.; Cooper, A.; Lilley, D. M. J. Biochemistry 2001, 40, 1423-1429; Borda, E. J.; Markley, J. C.; Sigurdsson, S. T. Nucleic Acids Res. 2003, 31, 2595-2600; Hampel, K. J.; Burke, J. M. Biochemistry 2003, 42, 4421-4429; Bondensgaard, K.; Mollova, E. T.; Pardi, A. Biochemistry 2002, 41, 11532-11542.
12. Rueda, D.; Wick, K.; McDowell, S. E.; Walter, N. G. Biochemistry 2003, 42, 9924-9936; Stage-Zimmermann, T. K.; Uhlenbeck, O. C. Nat. Struct. Biol. 2001, 8, 863-867; Curtis, E. A.; Bartel, D. P. RNA 2001, 7, 546-552; Hammann, C.; Cooper, A.; Lilley, D. M. J. Biochemistry 2001, 40, 1423-1429; Borda, E. J.; Markley, J. C.; Sigurdsson, S. T. Nucleic Acids Res. 2003, 31, 2595-2600; Hampel, K. J.; Burke, J. M. Biochemistry 2003, 42, 4421-4429; Bondensgaard, K.; Mollova, E. T.; Pardi, A. Biochemistry 2002, 41, 11532-11542.
13. Rueda, D.; Wick, K.; McDowell, S. E.; Walter, N. G. Biochemistry 2003, 42, 9924-9936; Stage-Zimmermann, T. K.; Uhlenbeck, O. C. Nat. Struct. Biol. 2001, 8, 863-867; Curtis, E. A.; Bartel, D. P. RNA 2001, 7, 546-552; Hammann, C.; Cooper, A.; Lilley, D. M. J. Biochemistry 2001, 40, 1423-1429; Borda, E. J.; Markley, J. C.; Sigurdsson, S. T. Nucleic Acids Res. 2003, 31, 2595-2600; Hampel, K. J.; Burke, J. M. Biochemistry 2003, 42, 4421-4429; Bondensgaard, K.; Mollova, E. T.; Pardi, A. Biochemistry 2002, 41, 11532-11542.
14. Rueda, D.; Wick, K.; McDowell, S. E.; Walter, N. G. Biochemistry 2003, 42, 9924-9936; Stage-Zimmermann, T. K.; Uhlenbeck, O. C. Nat. Struct. Biol. 2001, 8, 863-867; Curtis, E. A.; Bartel, D. P. RNA 2001, 7, 546-552; Hammann, C.; Cooper, A.; Lilley, D. M. J. Biochemistry 2001, 40, 1423-1429; Borda, E. J.; Markley, J. C.; Sigurdsson, S. T. Nucleic Acids Res. 2003, 31, 2595-2600; Hampel, K. J.; Burke, J. M. Biochemistry 2003, 42, 4421-4429; Bondensgaard, K.; Mollova, E. T.; Pardi, A. Biochemistry 2002, 41, 11532-11542.
15. Rueda, D.; Wick, K.; McDowell, S. E.; Walter, N. G. Biochemistry 2003, 42, 9924-9936; Stage-Zimmermann, T. K.; Uhlenbeck, O. C. Nat. Struct. Biol. 2001, 8, 863-867; Curtis, E. A.; Bartel, D. P. RNA 2001, 7, 546-552; Hammann, C.; Cooper, A.; Lilley, D. M. J. Biochemistry 2001, 40, 1423-1429; Borda, E. J.; Markley, J. C.; Sigurdsson, S. T. Nucleic Acids Res. 2003, 31, 2595-2600; Hampel, K. J.; Burke, J. M. Biochemistry 2003, 42, 4421-4429; Bondensgaard, K.; Mollova, E. T.; Pardi, A. Biochemistry 2002, 41, 11532-11542.
16. Rueda, D.; Wick, K.; McDowell, S. E.; Walter, N. G. Biochemistry 2003, 42, 9924-9936; Stage-Zimmermann, T. K.; Uhlenbeck, O. C. Nat. Struct. Biol. 2001, 8, 863-867; Curtis, E. A.; Bartel, D. P. RNA 2001, 7, 546-552; Hammann, C.; Cooper, A.; Lilley, D. M. J. Biochemistry 2001, 40, 1423-1429; Borda, E. J.; Markley, J. C.; Sigurdsson, S. T. Nucleic Acids Res. 2003, 31, 2595-2600; Hampel, K. J.; Burke, J. M. Biochemistry 2003, 42, 4421-4429; Bondensgaard, K.; Mollova, E. T.; Pardi, A. Biochemistry 2002, 41, 11532-11542.
17. DeRose, V. J. Curr. Opin. Struct. Biol. 2003, 13, 317-324; Hanna, R.; Doudna, J. A. Curr. Opin. Chem. Biol. 2000, 4, 166-170; Fedor, M. J. Curr. Opin. Struct. Biol. 2002, 12, 289-295.
18. DeRose, V. J. Curr. Opin. Struct. Biol. 2003, 13, 317-324; Hanna, R.; Doudna, J. A. Curr. Opin. Chem. Biol. 2000, 4, 166-170; Fedor, M. J. Curr. Opin. Struct. Biol. 2002, 12, 289-295.
19. DeRose, V. J. Curr. Opin. Struct. Biol. 2003, 13, 317-324; Hanna, R.; Doudna, J. A. Curr. Opin. Chem. Biol. 2000, 4, 166-170; Fedor, M. J. Curr. Opin. Struct. Biol. 2002, 12, 289-295.
20. Misra, V. K.; Draper, D. E. J. Mol. Biol. 2002, 317, 507-521; Misra, V. K.; Shiman, R.; Draper, D. E. Biopolymers 2003, 69, 118-136; Draper, D. E. RNA 2004, 10, 335-343.
21. Misra, V. K.; Draper, D. E. J. Mol. Biol. 2002, 317, 507-521; Misra, V. K.; Shiman, R.; Draper, D. E. Biopolymers 2003, 69, 118-136; Draper, D. E. RNA 2004, 10, 335-343.
22. Misra, V. K.; Draper, D. E. J. Mol. Biol. 2002, 317, 507-521; Misra, V. K.; Shiman, R.; Draper, D. E. Biopolymers 2003, 69, 118-136; Draper, D. E. RNA 2004, 10, 335-343.
23. Juneau, K.; Podell, E.; Harrington, D. J.; Cech, T. R. Structure 2001, 9, 221-231.
24. Levy, G. C. Nitrogen-15 Nuclear Magnetic Resonance Spectroscopy; John Wiley & Sons: New York, 1979.
25. Buchanan, G. W.; Stothers, J. B. Can. J. Chem. 1982, 60, 787-7791.
26. Markowski, V.; Sullivan, G. R.; Roberts, J. D. J. Am. Chem. Soc. 1977, 99, 714-718.
27. Wang, C.; Gao, H.; Gaffney, B. L.; Jones, R. A. J. Am. Chem. Soc. 1991, 113, 5486-5488.
28. Gao, X.; Jones, R. A. J. Am. Chem. Soc. 1987, 109, 3169-3171; Gaffney, B. L.; Goswami, B.; Jones, R. A. J. Am. Chem. Soc. 1993, 115, 12607-12608; Gaffney, B. L.; Kung, P.-P.; Wang, C.; Jones, R. A. J. Am. Chem. Soc. 1995, 117, 12281-12283.
29. Gao, X.; Jones, R. A. J. Am. Chem. Soc. 1987, 109, 3169-3171; Gaffney, B. L.; Goswami, B.; Jones, R. A. J. Am. Chem. Soc. 1993, 115, 12607-12608; Gaffney, B. L.; Kung, P.-P.; Wang, C.; Jones, R. A. J. Am. Chem. Soc. 1995, 117, 12281-12283.
30. Gao, X.; Jones, R. A. J. Am. Chem. Soc. 1987, 109, 3169-3171; Gaffney, B. L.; Goswami, B.; Jones, R. A. J. Am. Chem. Soc. 1993, 115, 12607-12608; Gaffney, B. L.; Kung, P.-P.; Wang, C.; Jones, R. A. J. Am. Chem. Soc. 1995, 117, 12281-12283.
31. Suzumura, K.; Yoshinari, K.; Tanaka, Y.; Takagi, Y.; Kasai, Y.; Warashina, M.; Kuwabara, T.; Orita, M.; Taira, K. J. Am. Chem. Soc. 2002, 124, 8230-8236; O'Rear, J. L.; Wang, S.; Feig, A. L.; Beigelman, L.; Uhlenbeck, O. C.; Herschlag, D. RNA 2001, 7, 537-545; Maderia, M.; Hunsicker, L. M.; DeRose, V. J. Biochemistry 2000, 39, 12113-12120.
32. Suzumura, K.; Yoshinari, K.; Tanaka, Y.; Takagi, Y.; Kasai, Y.; Warashina, M.; Kuwabara, T.; Orita, M.; Taira, K. J. Am. Chem. Soc. 2002, 124, 8230-8236; O'Rear, J. L.; Wang, S.; Feig, A. L.; Beigelman, L.; Uhlenbeck, O. C.; Herschlag, D. RNA 2001, 7, 537-545; Maderia, M.; Hunsicker, L. M.; DeRose, V. J. Biochemistry 2000, 39, 12113-12120.
33. Suzumura, K.; Yoshinari, K.; Tanaka, Y.; Takagi, Y.; Kasai, Y.; Warashina, M.; Kuwabara, T.; Orita, M.; Taira, K. J. Am. Chem. Soc. 2002, 124, 8230-8236; O'Rear, J. L.; Wang, S.; Feig, A. L.; Beigelman, L.; Uhlenbeck, O. C.; Herschlag, D. RNA 2001, 7, 537-545; Maderia, M.; Hunsicker, L. M.; DeRose, V. J. Biochemistry 2000, 39, 12113-12120.
34. Tanaka, Y.; Morita, E. H.; Hayashi, H.; Kasai, Y.; Tanaka, T.; Taira, K. J. Am. Chem. Soc. 2000, 122, 11303-11310.
35. Tanaka, Y.; Kasai, Y.; Mochizuki, S.; Wakisaka, A.; Morita, E. H.; Kojima, C.; Toyozawa, A.; Kondo, Y.; Taki, M.; Takagi, Y.; Inoue, A.; Yamasaki, K.; Taira, K. J. Am. Chem. Soc. 2004, 126, 744.
36. Tanaka, Y.; Kojima, C.; Morita, E. H.; Kasai, Y.; Yamasaki, K.; Ono, A.; Kainosho, M.; Taira, K. J. Am. Chem. Soc. 2002, 124, 4595-4601.
37. Sychrovsky, V.; Sponer, J.; Hobza, P. J. Am. Chem. Soc. 2004, 126, 663-672.
38. Rhee, Y.; Wang, C.; Gaffney, B. L.; Jones, R. A. J. Am. Chem. Soc. 1993, 115, 8742-8746; Zhang, X.; Gaffney, B. L.; Jones, R. A. J. Am. Chem. Soc. 1998, 120, 615-618; Zhang, X.; Gaffney, B. L.; Jones, R. A. J. Am. Chem. Soc. 1998, 120, 6625-6626.
39. Rhee, Y.; Wang, C.; Gaffney, B. L.; Jones, R. A. J. Am. Chem. Soc. 1993, 115, 8742-8746; Zhang, X.; Gaffney, B. L.; Jones, R. A. J. Am. Chem. Soc. 1998, 120, 615-618; Zhang, X.; Gaffney, B. L.; Jones, R. A. J. Am. Chem. Soc. 1998, 120, 6625-6626.
40. Rhee, Y.; Wang, C.; Gaffney, B. L.; Jones, R. A. J. Am. Chem. Soc. 1993, 115, 8742-8746; Zhang, X.; Gaffney, B. L.; Jones, R. A. J. Am. Chem. Soc. 1998, 120, 615-618; Zhang, X.; Gaffney, B. L.; Jones, R. A. J. Am. Chem. Soc. 1998, 120, 6625-6626.
41. Shallop, A. J.; Gaffney, B. L.; Jones, R. A. J. Org. Chem. 2003, 68, 8657-8661.
42. Zhao, H.; Pagano, A. R.; Wang, W.; Shallop, A.; Gaffney, B. L.; Jones, R. A. J. Org. Chem. 1997, 62, 7832-7835.
43. 15N chemical shift evidence of binding for this metal.