Methodology article

Revealing biases inherent in recombination protocols

Javier F Chaparro-Riggers^1* , Bernard LW Loo^1* , Karen M Polizzi¹ , Phillip R Gibbs^1,4 , Xiao-Song Tang³ , Mark J Nelson³ and Andreas S Bommarius^1,2

¹  School of Chemical and Biomolecular Engineering, Parker H. Petit Institute of Bioengineering and Bioscience, School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332-0363, USA

²  School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332-0363, USA

³  EI DuPont de Nemours & Company, PO Box 80328, Wilmington, DE 19880-0328, USA

⁴  Stheno Corporation, 311 Ferst Drive, Atlanta, 30332-0100, USA

author email corresponding author email* Contributed equally

BMC Biotechnology 2007, 7:77doi:10.1186/1472-6750-7-77

Published:	14 November 2007

Abstract

Background

The recombination of homologous genes is an effective protein engineering tool to evolve proteins. DNA shuffling by gene fragmentation and reassembly has dominated the literature since its first publication, but this fragmentation-based method is labor intensive. Recently, a fragmentation-free PCR based protocol has been published, termed recombination-dependent PCR, which is easy to perform. However, a detailed comparison of both methods is still missing.

Results

We developed different test systems to compare and reveal biases from DNA shuffling and recombination-dependent PCR (RD-PCR), a StEP-like recombination protocol. An assay based on the reactivation of β-lactamase was developed to simulate the recombination of point mutations. Both protocols performed similarly here, with slight advantages for RD-PCR. However, clear differences in the performance of the recombination protocols were observed when applied to homologous genes of varying DNA identities. Most importantly, the recombination-dependent PCR showed a less pronounced bias of the crossovers in regions with high sequence identity. We discovered that template variations, including engineered terminal truncations, have significant influence on the position of the crossovers in the recombination-dependent PCR. In comparison, DNA shuffling can produce higher crossover numbers, while the recombination-dependent PCR frequently results in one crossover. Lastly, DNA shuffling and recombination-dependent PCR both produce counter-productive variants such as parental sequences and have chimeras that are over-represented in a library, respectively. Lastly, only RD-PCR yielded chimeras in the low homology situation of GFP/mRFP (45% DNA identity level).

Conclusion

By comparing different recombination scenarios, this study expands on existing recombination knowledge and sheds new light on known biases, which should improve library-creation efforts. It could be shown that the recombination-dependent PCR is an easy to perform alternative to DNA shuffling.