Abstract
Site-directed mutagenesis has become an extremely powerful tool for the study of protein folding, protein-protein interactions, enzymatic catalysis, and other structure-function issues. Whereas this technique has had a major impact, it nonetheless has been limited to the 20 “proteinogenic” (standard) amino acids normally incorporated during ribosomal biosynthesis. This limitation has precluded the ability to site-specifically incorporate other amino acids that have been specifically designed to probe structure, function, or activity in novel ways. The ability to modify a protein by site-specifically introducing such non-standard amino acids with novel functionality would thus be useful in many investigations, but in addition, the ability to introduce nonstandard amino acids with more conservative modifications than are allowed by traditional site-directed mutagenesis (i.e., substitution of a single atom within an amino acid side chain) also could be quite useful.
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Bain, J. D., Glabe, C. G., Dix, T. A., Chamberlin, A. R., and Diala, E. S. (1989) Biosynthetic site-specific incorporation of a non-natural amino acid into a polypeptide. J. Am. Chem. Soc. 111, 8013–8014.
Noren, C. J., Anthony-Cahill, S. J., Griffith, M. C., and Schultz, P. G. (1989) A general method for site-specific incorporation of unnatural amino acids into proteins. Science 244, 182–188.
Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning. A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
Jones, R. A. (1984) Preparation of protected deoxyribonucleotides, in Oligonucleotide Synthesis (Gait, M. J., ed. ), IRL, Oxford, pp 23–27.
Uhlmann, E. and Engels, J. (1986) Chemical 5′-phosphorylation of oligonucleotides valuable in automated DNA synthesis. Tetrahedron Lett. 27, 1023–1026.
Heaphy, S., Singh, M., and Gatt, M. J. (1987) Effect of single amino acid changes in the region of the adenylation site of T4 RNA ligase. Biochemistry 26, 1688–1696.
Roesser, J. R., Xu, C., Payne, R. C., Surratt, C. K., and Hecht, S. M., (1989) Preparation of misacylated aminoacyl-tRNA(Phe)’s useful as probes of the ribosomal acceptor site. Biochemistry 28, 5185–5195.
Leinfelder, W., Zehelein, E., Mandrand-Berthelot, M. A., and Bock, A. (1988) Gene for a novel tRNA species that accepts 1-serine and cotranslationally inserts selenocysteine. Nature 331, 723–725.
Soll, D. (1988) Genetic code enter a new amino acid. Nature 331, 662–663.
Fersht, A. R. and Dingwall, C. (1979) Evidence for the double-sieve editing mechanism in protein synthesis. Steric exclusion of isoleucine by valyl-tRNA synthetases. Biochemistry 18, 2627–2631.
Bruce, A. G., Atkins, J. F., Wills, N., Uhlenbeck, O., and Gesteland, R. F. (1982) Replacement of anticodon loop nucleotides to produce functional tRNAs amber suppressors derived from yeast tRNAPhe. Proc. Natl. Acad. Sci. USA 79, 7127–7131.
Bruce, A. G. and Uhlenbeck, O. C. (1982) Enzymatic replacement of the anticodon of yeast phenylalanine transfer ribonucleic acid. Biochemistry 21, 855–861.
Bain, J. D., Wacker, D. A., Kuo, E. E., Lyttle, M. H., and Chamberlin, A. R. (1991) Preparation of chemically misacylated semisynthetic nonsense suppressor tRNAs employed in biosynthetic incorporation of non-natural residues into proteins. J. Org. Chem. 56, 4615–4625.
Noren, C. J., Anthony-Cahill, S. J., Suich, D. J., Noren, K. A., Griffith, M. C., and Schultz, P. G. (1990) In vitro suppression of an amber mutation by a chemically aminoacylated transfer RNA prepared by runoff transcription. Nuc. Acids Res. 18, 83–88.
Milligan, J. F., Groebe, D. R., Witherell, G. W., and Uhlenbeck, O. C. (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nuc. Acids Res. 15, 8783–8798.
McClain, W. H., Foss, K., Jenkins, R. A., and Schneider, J. (1991) Rapid determination of nucleotides that define tRNA(Gly) acceptor identity. Proc Natl. Acad. Sci. USA 88, 6147–6151.
Rosa, M. D. (1979) Four T7 RNA polymerase promoters contain an identical 23 bp sequence. Cell 16, 815–825.
Wacker, D. A. (1994) New Amino Acids for Protein Photoaffinity Labeling. Ph. D. Dissertation, University of California, Irvine.
Schenborn, E. T. and Mierendorf, R. C. J. (1985) A novel transcription property of SP6 and T7 RNA polymerases dependence on template structure. Nucleic Acids Res. 13, 6223–6236.
Robertson, S. A., Noren, C. J., Anthony-Cahill, S. J., Griffith, M. G., and Schultz, P. G. (1989) The use of 5′-phospho-2 deoxyribocytidylylriboadenosine as a facile route to chemical aminoacylation of tRNA. Nucleic Acids Res. 17, 9649–9660.
Gottikh, B. P., Krayevsky, A. A., Tarussova, N. B., Purygin, P. P., and Tsilevich, T. L. (1970) The general synthetic route to amino acid esters of nucleotides and nucleoside-5′-triphosphates and some properties of these compounds. Tetrahedron 26, 4419–4433.
Snopek, T. J., Sugino, A., Agarwal, K. L., and Cozzarelli, N. R. (1976) Catalysis of DNA joining by bacteriophage T4 RNA ligase. Biochem Biophys. Res. Comm. 68, 417–424.
Sugino, A., Snopek, T. J., and Cozzarelli, N. R. (1977) Bacteriophage T4 RNA ligase. Reaction intermediates and interaction of substrates. J. Biol. Chem. 252, 1732–1738.
Bruce, A. G. and Uhlenbeck, O. C. (1978) Reactions at the termini of tRNA with T4 RNA ligase. Nucl. Acids Res. 5, 3665–3677.
Baldini, G., Martoglio, B., Schachenmann, A., Zugliani, C., and Brunner, J. (1988) Mischarging Escherichia coli tRNAPhe with L-4′-[3-(trifluoromethyl)-3H-diazirin-3-yl]phenylalanine, a photoactivatable analogue of phenylalanine. Biochemistry 27, 7951–7959.
Lederman, M. and Zubay, G. (1967) DNA-directed peptide synthesis 1. A comparison of T2 and Escherichia coli DNA-directed peptide synthesis in two cell-free systems. Biochim Biophys. Acta 149, 253–258.
DeVries, J. K. and Zubay, G. (1967) DNA-directed peptide synthesis, II. The synthesis of the α-fragment of the enzyme β-galactosidase. Proc. Natl. Acad. Sci. USA 57, 1010–1012.
Zubay, G. (1973) In vitro synthesis of protein in microbial systems. Ann. Rev. Genet. 7, 267–287.
Collis, J. (1979) Cell-free synthesis of proteins coding for mobilization functions of ColE1 and transposition functions of Tn3. Gene 6, 29–42.
Pratt, J. M. (1984) Coupled transcription-translation in prokaryotic cell-free systems, in Transcription and Translation. A Practical Approach (Hanes, B. D. and Higgins, S. J., eds.), IRL, Oxford, pp. 179–209.
Artz, S. W. and Broach, J. R. (1975) Histidine regulation in salmonella typhimurium an activator-attenuator model of gene regulation. Proc. Natl. Acad. Sci. USA 72, 3453–3457.
Keener, J. W. (1989) Nitrogen Regulation in Enteric Bacteria Protein Kinase and Phosphoprotein Phosphatase Activities of the NTRB and NTRC Proteins. Ph.D. Dissertation, University of California, Davis
Bremer, H. and Dennis, P. P. (1987) Modulation of chemical composition and other parameters of the cell by growth rate, in Escherichia coli and Salmonella typhimurium Cellular and Molecular Biology (Neidhardt, F. C., ed. ), Am Soc Microbiol, Washington, DC, pp 1527–1542.
Yang, H. L., Ivashkiv, L., Chen, H. Z., Zubay, G., and Cashel, M. (1980) Cell-free coupled transcription-translation system for investigation of linear DNA segments. Proc. Natl. Acad. Sci. USA 77, 7029–7033.
Bywater, M., Bywater, R., and Hellman, L. (1983) A novel chromatographic procedure for purification of bacterial plasmids. Anal. Biochem. 132, 219–224.
Raymond, G. J., Bryant, P. G. I., Nelson, A., and Johnson, J. D. (1988) Large-scale isolation of covalently closed circular DNA using gel filtration chromatography. Anal. Biochem. 173, 125–133.
Miller, J. H. (1972) Experiments in Molecular Genetics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, p 403.
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Steward, L.E., Chamberlin, A.R. (1998). Protein Engineering with Nonstandard Amino Acids. In: Martin, R. (eds) Protein Synthesis. Methods in Molecular Biology, vol 77. Springer, Totowa, NJ. https://doi.org/10.1385/0-89603-397-X:325
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DOI: https://doi.org/10.1385/0-89603-397-X:325
Publisher Name: Springer, Totowa, NJ
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