In vitro selection for sense codon suppression

RNA

Volumn 9, Issue 7, 2003, Pages 780-786

  Frankel, Adam ^a   Roberts, Richard W ^a  

^a California Institute of Technology ^*  (United States)

Author keywords

mRNA display; Selection; Sense codon suppression; Translation; tRNA; Unnatural amino acid

Indexed keywords

ADENINE; AMINO ACID; BIOCYTIN; GUANINE; MESSENGER RNA; TRANSFER RNA; URACIL;

ANTICODON; ARTICLE; BASE PAIRING; GENE FUNCTION; GENE INSERTION; GENE LIBRARY; GENE PROBE; GENE REPRESSION; GENE SEQUENCE; GENETIC CODE; GENETIC ENGINEERING; GENETIC SELECTION; GENETIC VARIABILITY; IN VITRO STUDY; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; RNA STRUCTURE; RNA TRANSLATION; SEQUENCE ANALYSIS; STOP CODON; TECHNIQUE;

AMINO ACID SEQUENCE; BASE SEQUENCE; CODON; DNA, COMPLEMENTARY; GENETIC CODE; MOLECULAR SEQUENCE DATA; OLIGODEOXYRIBONUCLEOTIDES; PLASMIDS; RNA, ANTISENSE; RNA, MESSENGER; RNA, TRANSFER; TEMPLATES, GENETIC;

EID: 0038044525     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5350303     Document Type: Article

References (28)

1. Crick, F.H. 1966. Codon-anticodon pairing: The wobble hypothesis. J. Mol. Biol. 19: 548-555.
2. Dougherty, D.A. 2000. Unnatural amino acids as probes of protein structure and function. Curr. Opin. Chem. Biol. 4: 645-652.
3. Forster, A.C., Weissbach, H., and Blacklow, S.C. 2001. A simplified reconstitution of mRNA-directed peptide synthesis: Activity of the epsilon enhancer and an unnatural amino acid. Anal. Biochem. 297: 60-70.
4. Giege, R., Sissler, M., and Florentz, C. 1998. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res. 26: 5017-5035.
5. Heckler, T.G., Chang, L.H., Zama, Y., Naka, T., Chorghade, M.S., and Hecht, S.M. 1984. T4 RNA ligase mediated preparation of novel "chemically misacylated" tRNAPheS. Biochemistry 23: 1468-1473.
6. Hohsaka, T. and Sisido, M. 2002. Incorporation of non-natural amino acids into proteins. Curr. Opin. Chem. Biol. 6: 809-815.
7. Hohsaka, T., Sato, K., Sisido, M., Takai, K., and Yokoyama, S. 1994. Site-specific incorporation of photofunctional nonnatural amino acids into a polypeptide through in vitro protein biosynthesis. FEBS Lett. 344: 171-174.
8. Ibba, M. and Soll, D. 1999. Quality control mechanisms during translation. Science 286: 1893-1897.
9. Ikemura, T. and Ozeki, H. 1983. Codon usage and transfer RNA content: Organism-specific codon-choice patterns in reference to the isoacceptor contents. Cold Spring Harbor Symp. Quant. Biol. 47: 1087-1097.
10. Jackson, R.J. and Hunt, T. 1983. Preparation and use of nuclease-treated rabbit reticulocyte lysates for the translation of eukaryotic messenger RNA. Methods Enzymol. 96: 50-74.
11. Jackson, R.J., Napthine, S., and Brierley, I. 2001. Development of a tRNA-dependent in vitro translation system. RNA 7: 765-773.
12. Kanaya, S., Yamada, Y., Kinouchi, M., Kudo, Y., and Ikemura, T. 2001. Codon usage and tRNA genes in eukaryotes: Correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J. Mol. Evol. 53: 290-298.
13. LaRiviere, F.J., Wolfson, A.D., and Uhlenbeck, O.C. 2001. Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation. Science 294: 165-168.
14. Li, S., Millward, S., and Roberts, R. 2002. In vitro selection of mRNA display libraries containing an unnatural amino acid. J. Am. Chem. Soc. 124: 9972-9973.
15. Lim, V.I. and Curran, J.F. 2001. Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure. RNA 7: 942-957.
16. Marck, C. and Grosjean, H. 2002. tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA 8: 1189-1232.
17. Nakamura, Y., Ito, K., and Ehrenberg, M. 2000. Mimicry grasps reality in translation termination. Cell 101: 349-352.
18. Navarro, F. and Thuriaux, P. 2000. In vivo misreading by tRNA overdose. RNA 6: 103-110.
19. Ogle, J.M., Murphy, F.V., Tarry, M.J., and Ramakrishnan, V. 2002. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111: 721-732.
20. Parker, J. 1989. Errors and alternatives in reading the universal genetic code. Microbiol. Rev. 53: 273-298.
21. Roberts, R.W. 1999. Totally in vitro protein selection using mRNA-protein fusions and ribosome display. Curr. Opin. Chem. Biol. 3: 268-273.
22. Roberts, R.W. and Szostak, J.W. 1997. RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc. Natl. Acad. Sci. 94: 12297-12302.
23. Robertson, S.A., Ellman, J.A., and Schultz, P.G. 1991. A general and efficient route for chemical aminoacylation of transfer RNAs. J. Am. Chem. Soc. 113: 2722-2729.
24. Saks, M.E., Sampson, J.R., Nowak, M.W., Kearney, P.C., Du, F., Abelson, J.N., Lester, H.A., and Dougherty, D.A. 1996. An engineered Tetrahymena tRNAGln for in vivo incorporation of unnatural amino acids into proteins by nonsense suppression. J. Biol. Chem. 271: 23169-23175.
25. Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K., and Ueda, T. 2001. Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19: 751-755.
26. Tao, J. and Schimmel, P. 2000. Inhibitors of aminoacyl-tRNA synthetases as novel anti-infectives. Expert Opin. Investig. Drugs 9: 1767-1775.
27. Gln mutants that translate the CGA arginine codon as glutamine in Escherichia coli. RNA 4: 1514-1522.
28. Wang, L. and Schultz, P.G. 2002. Expanding the genetic code. Chem. Commun. (Camb.): 1-11.