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MINI REVIEW

Challenges of the genetic code for exploring sequence space in directed protein evolution

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Pages 229-241 | Published online: 11 Jul 2009

References

  • FH Arnold, Georgiou, G, 2003. Directed evolution library creation: Methods and protocols. New Jersey: Humana Press.
  • Barrell BG, Bankier AT, Drouin J. Different genetic-code in human mitochondria. Nature 1979; 282: 189–194
  • Cavalcanti ARO, Landweber LF. Genetic code. Curr Biol 2004; 14: R147–R147
  • Cline J, Hogrefe HH. Strategies 2000; 13: 157–162
  • Crick FH. The origin of the genetic code. J Mol Biol 1968; 38: 367–379
  • Di Giulio M. The origin of the genetic code: Theories and their relationships, a review. Biosystems 2005; 80: 175–184
  • Dunnill P. Triplet nucleotide–amino-acid pairing; a stereochemical basis for the division between protein and non-protein amino-acids. Nature 1966; 210: 1267–1267
  • Engelberg-Kulka H, Liu ZS, Li C, Reches M. An extended Escherichia coli “selenocysteine insertion sequence” (SECIS) as a multifunctional RNA structure. Biofactors 2001; 14: 61–68
  • Freeland SJ, Hurst LD. The genetic code is one in a million. J Mol Evol 1998; 47: 238–248
  • Hao B, Gong WM, Ferguson TK, James CM, Krzycki JA, Chan MK. A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science 2002; 296: 1462–1466
  • Hayes F. Transposon-based strategies for microbial functional genomics and proteomics. Annu Rev Genet 2003; 37: 3–29
  • Jestin JL. Degeneracy in the genetic code and its symmetries by base substitutions. Compt Rend Biol 2006; 329: 168–171
  • Knight RD, Landweber LF. Rhyme or reason: RNA–arginine interactions and the genetic code. Chem Biol 1998; 5: R215–R220
  • Knight RD, Freeland SJ, Landweber LF. Selection, history and chemistry: The three faces of the genetic code. Trends Biochem Sci 1999; 24: 241–247
  • Krzycki JA. The direct genetic encoding of pyrrolysine. Curr Opin Microbiol 2005; 8: 706–712
  • LinGoerke JL, Robbins DJ, Burczak JD. PCR-based random mutagenesis using manganese and reduced dNTP concentration. Biotechniques 1997; 23: 409–412
  • Murakami H, Hohsaka T, Sisido M. Random insertion and deletion of arbitrary number of bases for codon-based random mutation of DNAs. Nat Biotechnol 2002; 20: 76–81
  • Nirenberg M. Historical review: deciphering the genetic code – a personal account. Trends Biochem Sci 2004; 29: 46–54
  • Pelc SR, Welton MGE. Stereochemical relationship between coding triplets and amino-acids. Nature 1966; 209: 868–870
  • Raju TNK. The Nobel chronicles – 1968: Har Khorana (b 1922); Robert Holley (1922–93); Marshall Nirenberg (b 1927). Lancet 1999; 354: 690–690
  • Rumer YB. Codon systemization in genetic code. Doklady Akad Nauk SSSR 1966; 167: 1393–1394
  • Sonneborn TM. Degeneracy of the genetic code: Extents, nature and genetic implications. Evolving genes and proteins, V Bryson, HJ Vogel. Academic Press, New York 1965
  • Srinivasan G, James CM, Krzycki JA. Pyrrolysine encoded by UAG in Archaea: Charging of a UAG-decoding specialized tRNA. Science 2002; 296: 1459–1462
  • Stadtman TC. Selenium biochemistry. Annu Rev Biochem 1990; 59: 111–127
  • Taylor FJR, Coates D. The code within the codons. Biosystems 1989; 22: 177–187
  • Volles MJ, Lansbury PT, Jr. A computer program for the estimation of protein and nucleic acid sequence diversity in random point mutagenesis libraries. Nucleic Acids Res 2005; 33: 3667–3677
  • Woese CR. On the evolution of genetic code. Proc Natl Acad Sci USA 1965; 54: 1546–1552
  • Wong JTF. Role of minimization of chemical distances between amino-acids in the evolution of the genetic-code. Proc Natl Acad Sci USA 1980; 77: 1083–1086
  • Wong TS, Tee KL, Hauer B, Schwaneberg U. Sequence saturation mutagenesis (SeSaM): A novel method for directed evolution. Nucleic Acids Res 2004; e32
  • Wong TS, Tee KL, Hauer B, Schwaneberg U. Sequence saturation mutagenesis with tunable mutation frequencies. Analyt Biochem 2005; 341: 187–189
  • Wong TS, Roccatano D, Zacharias M, Schwaneberg U. A statistical analysis of random mutagenesis methods used for directed protein evolution. J Mol Biol 2006a; 355: 858–871
  • Wong TS, Zhurina D, Schwaneberg U. The diversity challenge in directed protein evolution. Combinat Chem High Throughput Screen 2006b; 9: 271–288

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