title: Economical analysis of saturation mutagenesis experiments.
abstract: Saturation mutagenesis is a powerful technique for engineering proteins, metabolic pathways and genomes. In spite of its numerous applications, creating high-quality saturation mutagenesis libraries remains a challenge, as various experimental parameters influence in a complex manner the resulting diversity. We explore from the economical perspective various aspects of saturation mutagenesis library preparation: We introduce a cheaper and faster control for assessing library quality based on liquid media; analyze the role of primer purity and supplier in libraries with and without redundancy; compare library quality, yield, randomization efficiency, and annealing bias using traditional and emergent randomization schemes based on mixtures of mutagenic primers; and establish a methodology for choosing the most cost-effective randomization scheme given the screening costs and other experimental parameters. We show that by carefully considering these parameters, laboratory expenses can be significantly reduced.
authors.affiliation: 1] Department of Organic Synthesis, Max-Planck-Institut für Kohlenforschung, Mulheim, 45470, Germany [2] Department of Chemistry, Philipps-Universität Marburg, 35032, Germany [3] Prokaryotic Small RNA Biology Group, Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, 35043, Germany [4] Landes-Offensive zur Entwicklung Wissenschafltich-ökonomischer Exzellenz (LOEWE) Centre for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032, Germany.
authors.forename: Carlos G
authors.initials: CG
authors.lastname: Acevedo-Rocha
authors.affiliation: 1] Department of Organic Synthesis, Max-Planck-Institut für Kohlenforschung, Mulheim, 45470, Germany [2] Department of Chemistry, Philipps-Universität Marburg, 35032, Germany.
authors.forename: Manfred T
authors.initials: MT
authors.lastname: Reetz
authors.affiliation: Department of Statistics, University of Haifa, Haifa, 31905, Israel.
authors.forename: Yuval
authors.initials: Y
authors.lastname: Nov
mesh_terms: D003362:Cost-Benefit Analysis; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics; D015723:Gene Library; D016296:Mutagenesis; D015202:Protein Engineering / Q000191:economics / Q000379:methods; D011786:Quality Control; D017422:Sequence Analysis, DNA
chemical_list: D003577:Cytochrome P-450 Enzyme System