Abstract
Although proteins can be artificially improved by random insertion and deletion mutagenesis methods, these procedures are technically difficult. Here we describe a simple method called random insertional–deletional strand exchange mutagenesis (RAISE). This method is based on gene shuffling and can be used to introduce a wide variety of insertions, deletions, and substitutions. RAISE involves three steps: DNA fragmentation, attachment of a random short sequence, and reconstruction. This yields unique mutants and can be a powerful technique for protein engineering.
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References
Antikainen NM, Martin SF (2005) Altering protein specificity: techniques and applications. Bioorg Med Chem 13:2701–2716
Otten LG, Quax WJ (2005) Directed evolution: selecting today’s biocatalysts. Biomol Eng 22:1–9
Robertson DE, Steer BA (2004) Recent progress in biocatalyst discovery and optimization. Curr Opin Chem Biol 8:141–149
Powell KA, Ramer SW, del Cardayre SB et al (2001) Directed evolution and biocatalysis. Angew Chem Int Ed Engl 40:3948–3959
Brakmann S (2001) Discovery of superior enzymes by directed molecular evolution. Chembiochem 2:865–871
Farinas ET, Bulter T, Arnold FH (2001) Directed enzyme evolution. Curr Opin Biotechnol 12:545–551
Goldsmith M, Tawfik DS (2013) Enzyme engineering by targeted libraries. Methods Enzymol 523:257–283
Goldsmith M, Tawfik DS (2012) Directed enzyme evolution: beyond the low-hanging fruit. Curr Opin Struct Biol 22:406–412
Wang M, Si T, Zhao H (2012) Biocatalyst development by directed evolution. Bioresour Technol 115:117–125
Neylon C (2004) Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution. Nucleic Acids Res 32:1448–1459
Leung DW, Chen E, Goeddel DV (1989) A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Technique 1:11–15
Shortle D, Sondek J (1995) The emerging role of insertions and deletions in protein engineering. Curr Opin Biotechnol 6:387–393
Jones DD (2005) Triplet nucleotide removal at random positions in a target gene: the tolerance of TEM-1 b-lactamase to an amino acid deletion. Nucleic Acids Res 33:e80
Baldwin AJ, Busse K, Simm AM et al (2008) Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx). Nucleic Acids Res 36:e77
Murakami H, Hohsaka T, Sisido M (2002) Random insertion and deletion of arbitrary number of bases for codon-based random mutation of DNAs. Nat Biotechnol 20:76–81
Pikkemaat MG, Janssen DB (2002) Generating segmental mutations in haloalkane dehalogenase: a novel part in the directed evolution toolbox. Nucleic Acids Res 30:e35
Hayes F, Hallet B (2000) Pentapeptide scanning mutagenesis: encouraging old proteins to execute unusual tricks. Trends Microbiol 8:571–577
Kim D, Rhee Y, Rhodes D et al (2005) Directed evolution and identification of control regions of ColE1 plasmid replication origins using only nucleotide deletions. J Mol Biol 351:763–775
Fujii R, Kitaoka M, Hayashi K (2006) RAISE: a simple and novel method of generating random insertion and deletion mutations. Nucleic Acids Res 34:e30
Stemmer WPC (1994) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370:389–391
Lewin B (1994) Gene. Oxford University Press, Oxford
Lewis SM (1994) The mechanism of V(D)J joining: lessons from molecular, immunological, and comparative analyses. In: Dixon FJ (ed) Advances in immunology, vol 56. Academic, San Diego, pp 27–150
Komori T, Okada A, Stewart V et al (1993) Lack of N regions in antigen receptor variable region genes of TdT-deficient lymphocytes. Science 261:1171–1175
Pascarella S, Argos P (1992) Analysis of insertions/deletions in protein structures. J Mol Biol 224:461–471
Lorimer IAJ, Pastan I (1995) Random recombination of antibody single chain Fv sequences after fragmentation with DNaseI in the presence of Mn2+. Nucleic Acids Res 23:3067–3068
Aharoni A, Griffiths AD, Tawfik DS (2005) High-throughput screens and selections of enzyme-encoding genes. Curr Opin Chem Biol 9:210–216
Goddard JP, Reymond JL (2004) Recent advances in enzyme assays. Trends Biotechnol 22:363–370
Goddard JP, Reymond JL (2004) Enzyme assays for high-throughput screening. Curr Opin Biotechnol 15:314–322
Schmidt M, Bornscheuer UT (2005) High-throughput assays for lipases and esterases. Biomol Eng 22:51–56
Acknowledgments
This study was supported in part by a grant from the Program for Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN).
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Fujii, R., Kitaoka, M., Hayashi, K. (2014). Random Insertional–Deletional Strand Exchange Mutagenesis (RAISE): A Simple Method for Generating Random Insertion and Deletion Mutations. In: Gillam, E., Copp, J., Ackerley, D. (eds) Directed Evolution Library Creation. Methods in Molecular Biology, vol 1179. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-1053-3_10
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DOI: https://doi.org/10.1007/978-1-4939-1053-3_10
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