RNA aptamers to the peptidyl transferase inhibitor chloramphenicol

Chemistry and Biology

Volumn 4, Issue 11, 1997, Pages 833-843

  Burke, Donald H ^a   Hoffman, David C ^a,b   Brown, Analisa ^a   Hansen, Mark ^a   Pardi, Arthur ^a   Gold, Larry ^a,c  

^a UNIVERSITY OF COLORADO   (United States)

^b INSERM   (France)

^c GILEAD SCIENCES   (United States)

Author keywords

Chloramphenicol; Peptidlyl transfer; Ribosomal RNA structure; SELEX; Translation

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 0031278397     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(97)90116-2     Document Type: Article

References (41)

1. Tuerk, C. & Gold, L (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510.
2. Ellington, A.D. & Szostak, J.W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822.
3. Gold, L., Polisky, B., Uhlenbeck, O. & Yarus, M. (1995). Diversity of oligonucleotide functions. Annu. Rev. Biochem. 64, 763-797.
4. Cech, T.R. & Szewczak, A.A. (1996). Selecting apt RNAs for NMR. RNA 2: 625-627.
5. Dieckmann, T.S., Suzuki, E., Nakamura, G.K., & Feigon, J. (1996). Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA 2, 628-640.
6. Jiang, F., Kumar, R.A., Jones, R.A. & Patel, D.J. (1996). Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature 382, 183-186.
7. Yang, Y.K., M., Burgstaller, P., Westhof, E. & Famulok, M. (1996). Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science 272, 1343-1347.
8. Zimmermann, G.R., Jenison, R.D., Wick, C.L., Simorre, J.P. & Pardi, A. (1997). Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nat. Struct. Biol. 4, 644-649.
9. Macaya, R.F, Schultze, P., Smith, F.W., Roe, J.A. & Feigon, J. (1993). Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution. Proc. Natl Acad. Sci. USA 90, 3745-3749.
10. Morris, K.N. & Wool, I.G. (1994) Analysis of the contribution of an amphiphilic alpha-helix to the structure and to the function of ricin A chain. Proc. Natl. Acad. Sci. USA 91, 7530-7533.
11. Cimino, G.D., Gamper, H.B., Isaacs, S.T. & Hearst, J.E. (1985). Psoralens as photoactive probes of nucleic acid structure and function: organic chemistry, photochemistry, and biochemistry. Annu. Rev. Biochem. 54, 1151-1194.
12. Absalon, M.J., Wu, W., Kozarich, J.W. & Stubbe, J. (1995). Sequence-specific double-strand cleavage of DNA by Fe-bleomycin. 2. Mechanism and dynamics. Biochemistry 34, 2076.
13. Burger, R.M., Drlica, K., & Birdsall, B. (1994). The DNA cleavage pathway of iron bleomycin. Strand scission precedes deoxyribose 3-phosphate bond cleavage. J. Biol. Chem. 269, 25978-25985.
14. Rentzeperis, D., Marky, L. A., Dwyer, T. J., Geierstanger, B. H., Pelton, J.G. & Wemmer, D.E. (1995). Interaction of minor groove ligands to an AAATT/AATTT site: correlation of thermodynamic characterization and solution structure. Biochemistry 34, 2937-2945.
15. Zaug, A.J., Been, M.D., & Cech, T.R. (1986). The Tetrahymena ribozyme acts like an RNA restriction endonuclease. Nature 324, 429-433.
16. Schnare, M.N., Damberger, S.H., Gray, M.W. & Gutell, R.R. (1996). Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23S-like) ribosomal RNA. J. Mol. Biol. 256, 701-719.
17. Egebjerg, J., Larsen, N. & Garrett, R.A. (1990). Structural map of 23S rRNA, in The Ribosome: Structure, Function and Evolution. (Hill, W. E. et al. eds). pp. 168-179, American Society for Microbiology Press, Washington, DC.
18. Welch, M., Chastang, J. & Yarus, M. (1995). An inhibitor of ribosomal peptidyl transferase using transition-state analogy. Biochemistry 34, 385-390.
19. Barta, A., Steiner, G., Brosius, J. & Noller, H.F. (1984) Identification of a site on 23S ribosomal RNA located at the peptidyl transferase center. Proc. Natl Acad. Sci. USA 81, 3607-3611.
20. Vester, B. & Garrett, R.A. (1988). The importance of highly conserved nucleotides in the binding region of chloramphenicol at the peptidyl transfer centre of Escherichia coli 23S ribosomal RNA. EMBO J. 7, 3577-3587.
21. Douthwaite, S. (1992). Functional interactions within 23S rRNA involving the peptidyltransferase center. J. Bacteriol. 174, 1333-1338.
22. Ofengand, J., Ciesiolka, J., Denman, R. & Nurse, K. (1986). Structural and functional interactions of the tRNA-ribosome complex, in Structure, Function, and Genetics of Ribosomes. (Hardesty, B. & Kramer, G., eds) pp. 473-494, Springer-Verlag, New York.
23. Rodriguez-Fonseca, C., Amils, R. & Garrett, R.A. (1995). Fine structure of the peptidyl transferase centre on 23S-like rRNAs deduced from chemical probing of antibiotic-ribosome complexes. J. Mol. Biol. 247, 224-235.
24. Moazed, D. & Noller, H.F. (1987).Chloramphenicol, erythromycin, carbomycin, and vernamycin B protect overlapping sites in the peptidyl transferase region of 23S ribosomal RNA. Biochimie 69, 879-884.
25. Moazed, D. & Noller, H.F. (1989). Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E. sites. Cell 57, 585-597.
26. Noller, H.F. (1991). Ribosomal RNA and translation. Annu. Rev. Biochem. 60, 191-227.
27. Leviev, I.G., et al. & Mankin, S. (1994). A conserved secondary structural motif in 23S rRNA defines the site of interaction of amicetin, a universal inhibitor of peptide bond formation. EMBO J. 13, 1682-1686.
28. Jenison, R.D., Gill, S.C., Pardi, A. & Polisky, B. (1994). High-resolution molecular discrimination by RNA. Science 263, 1425-1429.
29. Connell, G.J., Illangesekare, M. & Yarus, M. (1993). Three small ribooligonucleotides with specific arginine sites. Biochemistry 32, 5497-5502.
30. Wallis, M.G., von Ahsen, U., Schroeder, R. & Famulok, M. (1995). A novel RNA motif for neomycin recognition. Chem. Biol. 2, 543-552.
31. Coutsogeorgopoulus, C. (1966). On the mechanism of action of chloramphenicol in protein synthesis. Biochim. Biophys. Acta 129, 214-217.
32. Zemlicka, J., Fernando-Moyano, M.C., Ariatti, M., Zurenko, G.E., Grady, J.E. & Ballesta, J.P.G. (1993). Hybrids of antibiotics inhibiting protein synthesis: synthesis and biological activity. J. Med. Chem. 36, 1239-1244.
33. Drainas, D., Mamos, P. & Coutsogeorgopolous, C. (1993). Aminoacyl analogs by chloramphenicol: examination of the kinetics of inhibition of peptide bond formation. J. Med. Chem. 36, 3542-3545.
34. Bhuta, P., Chung, H. L., Hwang, J.-S. & Zemlicka, J. (1980). Analogs of chloramphenicol: circular dichroism spectra, inhibition of ribosomal peptidyltransferase, and possible mechanism of action. J. Med Chem. 23, 1299-1305.
35. Spirin, A.S. & Lim, V.I. (1986). Stereochemical analysis of ribosomal transpeptidation, translocation and nacent peptide folding. In Structure, Function and Genetics of Ribozymes (Hardesty, B. & Kramer, G., eds), Springer-Verlag, New York.
36. Welch, M., Majerfeld, I. & Yarus, M. (1997). 23S rRNA similarity from selection for peptidyl transferase mimicry. Biochemistry 36: 6614-6623.
37. Burke, D.H., Scates, L.A., Andrews, K. & Gold, L. (1996). Bent pseudoknots and novel RNA inhibitors of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase. J. Mol. Biol. 264, 650-666.
38. Milligan, J.F., Groebe, D.R., Witherel, G.W. & Uhlenbeck, O.D. (1987). Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic. Acids. Res. 15, 8783.
39. Fasman, G.D. (1975). Handbook of Biochemistry and Molecular Biology, Volume 1: Nucleic Acids. CRC Press Inc., Cleveland.
40. Piotto, M., Saudek, V. and Sklenar, V. (1992). Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR 2, 661-665.
41. Wu, M., McDowell, J.A. & Turner, D.H. (1995). A periodic table of symmetric tandem mismatches in RNA. Biochemistry 34, 3204-3211.