title: Fold or hold: experimental evolution in vitro.
abstract: We introduce a system for experimental evolution consisting of populations of short oligonucleotides (Oli populations) evolving in a modified quantitative polymerase chain reaction (qPCR). It is tractable at the genetic, genomic, phenotypic and fitness levels. The Oli system uses DNA hairpins designed to form structures that self-prime under defined conditions. Selection acts on the phenotype of self-priming, after which differences in fitness are amplified and quantified using qPCR. We outline the methodological and bioinformatics tools for the Oli system here and demonstrate that it can be used as a conventional experimental evolution model system by test-driving it in an experiment investigating adaptive evolution under different rates of environmental change.
authors.affiliation: Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
authors.forename: S
authors.initials: S
authors.lastname: Collins
authors.forename: A
authors.initials: A
authors.lastname: Rambaut
authors.forename: S J
authors.initials: SJ
authors.lastname: Bridgett
mesh_terms: D019295:Computational Biology / Q000379:methods; D019020:Directed Molecular Evolution; D016296:Mutagenesis; D009841:Oligonucleotides / Q000737:chemistry; D060888:Real-Time Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D009841:Oligonucleotides
keywords: DNA hairpin; adaptation; aptamer; experimental evolution; polymerase chain reaction