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In vitro 'sexual' evolution through the PCR-based staggered extension process (StEP)

Abstract

This protocol describes a directed evolution method for in vitro mutagenesis and recombination of polynucleotide sequences. The staggered extension process (StEP) is essentially a modified PCR that uses highly abbreviated annealing and extension steps to generate staggered DNA fragments and promote crossover events along the full length of the template sequence(s). The resulting library of chimeric polynucleotide sequence(s) is subjected to subsequent high-throughput functional analysis. The recombination efficiency of the StEP method is comparable to that of the most widely used in vitro DNA recombination method, DNA shuffling. However, the StEP method does not require DNA fragmentation and can be carried out in a single tube. This protocol can be completed in 4–6 h.

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Acknowledgements

We thank the Department of Defense (N000140210725), National Science Foundation (BES-0348107), National Institutes of Health, and DuPont for supporting our work on development and applications of new directed evolution tools for protein science and engineering and metabolic engineering.

Author information

H.Z., first draft of the manuscript; W.Z., Box 2, Fig. 2, part of the Introduction and Anticipated Results; both authors participated in the editing and revision of the manuscript.

Correspondence to Huimin Zhao.

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The authors declare no competing financial interests.

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Further reading

Figure 1: Principle of the StEP method.
Figure 2: Scheme of the GFP-based recombination test system.

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