Deciphering RNA recognition: Aminoglycoside binding to the hammerhead ribozyme

Chemistry and Biology

Volumn 5, Issue 11, 1998, Pages

  Tor, Yitzhak ^a   Hermann, Thomas ^b   Westhof, Eric ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOGLYCOSIDE; AMMONIA; ELECTROSTATIC FIELD; METAL ION; PROTEIN FOLDING; PROTEIN INHIBITION; PROTEIN SYNTHESIS; RIBOZYME; RNA RECOGNITION; RNA SPLICING;

EID: 0032212026     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(98)90286-1     Document Type: Article

References (39)

1. Hermann, T. & Westhof, E. (1998). RNA as a drug target: chemical, modelling and evolutionary tools. Curr. Opin, Biotechnol. 9, 66-73.
2. Chow, C.S. & Bogdan, F.M. (1997). A structural basis for RNA-ligand interactions. Chem. Rev. 97, 1489-1513.
3. Michael, K. & Tor, Y. (1998). Designing novel RNA binders. Chem. Eur. J. 4, 2091-2098
4. Draper, D.E. (1992). The RNA-folding problem. Accounts Chem. Res. 25, 201-207.
5. Brion, P. & Westhof, E. (1997). Hierarchy and dynamics of RNA folding. Annu. Rev. Biophys. Biomol, Struct. 26, 113-137.
6. Moazed, D. & Noller, H.F. (1987). Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature 327, 389-394.
7. von Ahsen, U., Davies, J. & Schroeder, R. (1991). Antibiotic inhibition of group I ribozyme function. Nature 353, 368-370.
8. von Ahsen, U., Davies, J. & Schroeder, R. (1992). Non-competitive inhibition of group I intron RNA self-splicing by aminoglycoside antibiotics. J. Mol. Bol. 226, 935-941.
9. Stage, T.K., Hertel, K.J. & Uhlenbeck, O.G. (1995). Inhibition of the hammerhead ribozyme by neomycin. RNA 1, 95-101.
10. Rogers, J., Chang, A.H., von Ahsen, U., Schroeder, R. & Davies J. (1996). Inhibition of the self-cleavage reaction of the human hepatitis delta virus ribozyme by antibiotics. J. Mol. Biol. 259, 916-925.
11. Zapp, M.L., Stern, S. & Green, M.R. (1993). Small molecules that selectively block RNA binding of HIV-1 rev protein inhibit rev function and viral production. Cell 74, 969-978.
12. Mei, H.-Y., et al., & Czarnik A.W. (1995). Inhibition of an HIV-Tatderived peptide binding to Tar RNA by aminoglycosides antibiotics. Bioorg. Med. Chem. Lett. 5, 2755-2760.
13. Noller, H.F. (1991). Drugs and the RNA world. Nature, 353, 302-303.
14. Wallis, M.G. & Schroeder, R. (1997). The binding of antibiotics to RNA. Prog. Biophys. Molec. Biol. 67, 141-154.
15. Wallis, M.G., von Ahsen, U., Schroeder, R. & Famulok, M. (1995). A novel RNA motif for neomycin recognition. Chem. Biol. 2, 543-552.
16. Lato, S.M., Boles, A.R. & Ellington, A.D. (1995). In vitro selection of RNA lectins: using combinatorial chemistry to interpret ribozyme evolution. Chem. Biol. 2, 291-303.
17. Wang, Y. & Rando, R. (1995). Specific binding of aminoglycoside antibiotics to RNA. Chem. Biol. 2, 281-290.
18. Jiang, L., Suri, A.K., Fiala, R. & Patel, D.J. (1997). Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex. Chem. Biol. 4, 35-50.
19. Fourmy, D., Recht, M.I., Blanchard, S.C. & Puglisi, J.D. (1996). Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science 274, 1367-1371
20. Alper, P.B., Hendrix, M., Sears, P. & Wong, C.-H. (1998). Probing the specificity of aminoglycoside-ribosomal RNA interactions with designed synthetic analogs. J. Am. Chem. Soc. 120, 1965-1978.
21. Hendrix, M., Priestley, E.S., Joyce, J.F. & Wong, C.-H. (1997). Direct observation of aminoglycoside-RNA interactions by surface plasmon resonance. J. Am. Chem. Soc. 119, 3641-3648.
22. Wang, Y., Killian, J., Hamasaki, K. & Rando, R.R. (1996). RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities. Biochemistry 35, 12338-12346.
23. Wang, Y., Hamasaki, K. & Rando, R.R. (1997). Specificity of aminoglycoside binding to RNA constructs derived from the 16S rRNA decoding region and the HIV-RRE activator region. Biochemistry 36, 768-779.
24. Uhlenbeck, O.C. (1987). A small catalytic oligoribonucleotide. Nature 328, 596-600.
25. Clouet-d'Orval, B., Stage, T.K. & Uhlenbeck, O.C. (1995). Neomycin inhibition of the hammerhead ribozyme involves ionic interactions. Biochemistry 34, 11186-11190.
26. Pley, H.W., Flaherty, K.M. & McKay, D.B. (1994). Three-dimensional structure of a hammerhead ribozyme. Nature 372, 68-74.
27. Scott, W.G., Finch, J.T. & Klug, A. (1995). The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell 81, 991-1002.
28. Scott, W.G., Murray, J.B., Arnold, J.R.P., Stoddard, B.L. & Klug, A. (1996). Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science 274, 2065-2069.
29. 15N Nuclear magnetic resonance spectroscopy. The nebramycin aminoglycosides. J. Am. Chem. Soc. 98, 6885-6888.
30. Botto, R.E., Coxon, B. (1983). Nitrogen-15 nuclear magnetic resonance spectroscopy of neomycin B and related aminoglycosides. J. Am. Chem. Soc. 105, 1021-1028.
31. Szilágyi, L., Sz. Pusztahelyi, Z., Jakab, S. & Kovács, I. (1993). Microscopic protonation constants in tobramycin. An NMR and pH study with the aid of partially N-acetylated derivatives Carbohyd. Res. 247, 99-109.
32. Purohit, P. & Stern, S. (1994). Interactions of a small RNA with antibiotic and RNA ligands in the 30S subunit. Nature 370, 659-662.
33. Wang, H. & Tor, Y. (1998). RNA-aminoglycoside interactions: design, synthesis and binding of "amino-aminoglycosides" to RNA. Angew. Chem. Int. Ed. 37, 109-111.
34. Wang, H. & Tor, Y. (1997). Electrostatic interactions in RNA-aminoglycoside binding. J. Am. Chem. Soc. 119, 8734-8735.
35. Lide, D.R. Ed. CRC Handbook of Chemistry and Physics, pp. 8-45, 75th Edition, 1994.
36. Hermann, T. & Westhof, E. (1998). Aminoglycoside binding to the hammerhead ribozyme: a general model for the interaction of cationic antibiotics with RNA. J. Mol. Biol. 276, 903-912.
37. Hermann, T., Auffinger, P. & Westhof, E. (1998). Molecular dynamics investigations of hammerhead ribozyme RNA. Eur. Biophys. J. 27, 153-165.
38. Hermann, T. & Westhof, E. (1998). Exploration of metal ion binding sites in RNA folds with Brownian dynamics simulations. Structure 6, 1303-1315.
39. Nicholls, A., Sharp, K.A. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-96.