MDC-Analyzer: A novel degenerate primer design tool for the construction of intelligent mutagenesis libraries with contiguous sites

BioTechniques

Volumn 56, Issue 6, 2014, Pages 301-310

  Tang, Lixia ^a   Wang, Xiong ^a   Ru, Beibei ^a   Sun, Hengfei ^a   Huang, Jian ^a   Gao, Hui ^a  

^a UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Contiguous sites; Data driven protein engineering; Intelligent library design; Partial randomization

Indexed keywords

CONTIG; CODON; PRIMER DNA; PROTEIN;

AMINO ACID SEQUENCE; ANALYZER; ARTICLE; GENE MUTATION; LIBRARY; MUTAGENESIS; NONHUMAN; POLYMERASE CHAIN REACTION; PROTEIN ENGINEERING; SEQUENCE ANALYSIS; ANIMAL; CHEMISTRY; CODON; DEVICES; GENE LIBRARY; GENETICS; HUMAN; NUCLEOTIDE SEQUENCE; PROCEDURES;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CODON; DNA PRIMERS; GENE LIBRARY; HUMANS; MUTAGENESIS; PROTEIN ENGINEERING; PROTEINS;

EID: 84902332122     PISSN: 07366205     EISSN: 19409818     Source Type: Journal    
DOI: 10.2144/000114177     Document Type: Article

References (39)

1. Chen, K. and F. H. Arnold. 1993. Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. Proc. Natl. Acad. Sci. USA 90: 5618-5622.
2. Liao, H., T. McKenzie, and R. Hageman. 1986. Isolation of a thermostable enzyme variant by cloning and selection in a thermophile. Proc. Natl. Acad. Sci. USA 83: 576-580.
3. Arnold, F. H. and A. A. Volkov. 1999. Directed evolution of biocatalysts. Curr. Opin. Chem. Biol. 3: 54-59.
4. Turner, N. J. 2009. Directed evolution drives the next generation of biocatalysts. Nat. Chem. Biol. 5: 567-573.
5. Lutz, S. 2010. Beyond directed evolution-semi-rational protein engineering and design. Curr. Opin. Biotechnol. 21: 734-743.
6. Chica, R. A., N. Doucet, and J. N. Pelletier. 2005. Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. Curr. Opin. Biotechnol. 16: 378-384.
7. Fox, R. J. and G. W. Huisman. 2008. Enzyme optimization: moving from blind evolution to statistical exploration of sequence-function space. Trends Biotechnol. 26: 132-138.
8. Reetz, M. T., L. W. Wang, and M. Bocola. 2006. Directed evolution of enantioselective enzymes: iterative cycles of CASTing for probing protein-sequence space. Angew. Chem. Int. Ed. Engl. 45: 1236-1241.
9. Reetz, M. T. and J. D. Carballeira. 2007. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat. Protoc. 2: 891-903.
10. Reetz, M. T., M. Bocola, L. W. Wang, J. Sanchis, A. Cronin, M. Arand, J. Zou, A. Archelas, et al. 2009. Directed evolution of an enantioselective epoxide hydrolase: uncovering the source of enantioselectivity at each evolutionary stage. J. Am. Chem. Soc. 131: 7334-7343.
11. Neuner, P., R. Cortese, and P. Monaci. 1998. Codon-based mutagenesis using dimer-phosphoramidites. Nucleic Acids Res. 26: 1223-1227.
12. Virnekäs, B., L. Ge, A. Plückthun, K. C. Schneider, G. Wellnhofer, and S. E. Moroney. 1994. Trinucleotide phosphoramidites: ideal reagents for the synthesis of mixed oligonucleotides for random mutagenesis. Nucleic Acids Res. 22: 5600-5607.
13. Tang, L., H. Gao, X. Zhu, X. Wang, M. Zhou, and R. Jiang. 2012. Construction of "small-intelligent" focused mutagenesis libraries using well-designed combinatorial degenerate primers. Biotechniques 52: 149-158.
14. Kille, S., C. G. Acevedo-Rocha, L. P. Parra, Z. G. Zhang, D. J. Opperman, M. T. Reetz, and J. P. Acevedo. 2013. Reducing codon redundancy and screening effort of combinatorial protein libraries created by saturation mutagenesis. ACS Synth Biol 2: 83-92.
15. Tang, L., X. Zhu, H. Zheng, R. Jiang., and M. Majeric Elenkov. 2012. Key residues for controlling enantioselectivity of Halohydrin dehalogenase from Arthrobacter sp. strain AD2, revealed by structure-guided directed evolution. Appl. Environ. Microbiol. 78: 2631-2637.
16. Chaparro-Riggers, J. F., K. M. Polizzi, and A. S. Bommarius. 2007. Better library design: data-driven protein engineering. Biotechnol. J. 2: 180-191.
17. Davids, T., M. Schmidt, D. Böttcher, and U. T. Bornscheuer. 2013. Strategies for the discovery and engineering of enzymes for biocatalysis. Curr. Opin. Chem. Biol. 17: 215-220.
18. Voigt, C. A., C. Martinez, Z. G. Wang, S. L. Mayo, and F. H. Arnold. 2002. Protein building blocks preserved by recombination. Nat. Struct. Biol. 9: 553-558.
19. Saraf, M. C., A. R. Horswill, S. J. Benkovic, and C. D. Maranas. 2004. FamClash: A method for ranking the activity of engineered enzymes. Proc. Natl. Acad. Sci. USA 101: 4142-4147.
20. Meyer, M. M., L. Hochrein, and F. H. Arnold. 2006. Structure-guided SCHEMA recombination of distantly related b-lactamases. Protein Eng. Des. Sel. 19: 563-570.
21. Heinzelman, P., R. Komor, A. Kanaan, P. Romero, X. Yu, S. Mohler, C. Snow, and F. H. Arnold. 2010. Efficient screening of fungal cellobiohydrolase class I enzymes for thermostabilizing sequence blocks by SCHEMA structure-guided recombination. Protein Eng. Des. Sel. 23: 871-880.
22. Romero, P. A., E. Stone, C. Lamb, L. Chantranupong, A. Krause, A. E. Miklos, R. A. Hughes, B. Fechtel, et al. 2012. SCHEMA-designed variants of human Arginase I and II reveal sequence elements important to stability and catalysis. ACS Synth Biol 1: 221-228.
23. Pavelka, A., E. Chovancova, and J. Damborsky. 2009. HotSpot Wizard: a web server for identification of hot spots in protein engineering. Nucleic Acids Res. 37: W376-W383.
24. Glaser, F., Y. Rosenberg, A. Kessel, T. Pupko, and N. Ben-Tal. 2005. The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins 58: 610-617.
25. Jochens, H. and U. T. Bornscheuer. 2010. Natural diversity to guide focused directed evolution. ChemBioChem 11: 1861-1866.
26. Jochens, H., D. Aerts, and U. T. Bornscheuer. 2010. Thermostabilization of an esterase by alignment-guided focussed directed evolution. Protein Eng. Des. Sel. 23: 903-909.
27. Nobili, A., M. G. Gall, I. V. Pavlidis, M. L. Thompson, M. Schmidt, and U. T. Bornscheuer. 2013. Use of 'small but smart' libraries to enhance the enantioselectivity of an esterase from Bacillus stearothermophilus towards tetrahydrofuran-3-yl acetate. FEBS J. 280: 3084-3093.
28. Nov, Y. and D. Segev. 2013. Optimal codon randomization via mathematical programming. J. Theor. Biol. 335: 147-152.
29. Hughes, M. D., D. A. Nagel, A. F. Santos, A. J. Sutherland, and A. V. Hine. 2003. Removing the redundancy from randomised gene libraries. J. Mol. Biol. 331: 973-979.
30. Ashraf, M., L. Frigotto, M. E. Smith, S. Patel, M. D. Hughes, A. J. Poole, H. R. Hebaishi, C. G. Ullman, and A. V. Hine. 2013. ProxiMAX randomization: a new technology for non-degenerate saturation mutagenesis of contiguous codons. Biochem. Soc. Trans. 41: 1189-1194.
31. Reetz, M. T. and S. Wu. 2008. Greatly reduced amino acid alphabets in directed evolution: making the right choice for saturation mutagenesis at homologous enzyme positions. Chem. Commun. (Camb.) 43: 5499-5501.
32. Hogrefe, H. H., J. Cline, G. L. Youngblood, and R. M. Allen. 2002. Creating randomized amino acid libraries with the QuikChange™ multi site-directed mutagenesis kit. Biotechniques 33: 1158-1160.
33. Miyazaki, K. and M. Takenouchi. 2002. Creating random mutagenesis libraries using megaprimer PCR of whole plasmid. Biotechniques 33: 1033-1034.
34. Patrick, W. M., A. E. Firth, and J. M. Blackburn. 2003. User friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. Protein Eng. 16: 451-457.
35. Mena, M. A. and P. S. Daugherty. 2005. Automated design of degenerate codon libraries. Protein Eng. Des. Sel. 18: 559-561.
36. Tseng, W. C., J. W. Lin, T. Y. Wei, and T. Y. Fang. 2008. A novel megaprimed and ligase-free, PCR-based, site-directed mutagenesis method. Anal. Biochem. 375: 376-378.
37. Sanchis, J., L. Fernández, J. D. Carballeira, J. Drone, Y. Gumulya, H. Höbenreich, D. Kahakeaw, S. Kille, et al. 2008. Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates. Appl. Microbiol. Biotechnol. 81: 387-397.
38. Pai, J. C., K. C. Entzminger, and J. A. Maynard. 2012. Restriction enzyme-free construction of random gene mutagenesis libraries in Escherichia coli. Anal. Biochem. 421: 640-648.
39. Tang, L., K. Zheng, Y. Liu, Z. Zheng, H. Wang, C. Song, and H. Zhou. 2013. Exploring the potential of megaprimer PCR in coupling with orthogonal array design for mutagenesis library. Biotechnol. Appl. Biochem. 60: 190-195.