title: Dynamics of DNA in vitro evolution with Mnt-repressor: simulations and analysis.
abstract: The dynamics of DNA in vitro evolution with Mnt-repressor has been studied numerically and analytically. Based on experimental data and realistic energy landscape for DNA-Mnt-repressor interaction, we investigated the dynamics of DNA in vitro evolution using stochastic simulations. The binding energy of DNA to Mnt-repressor was considered to consist of two parts: the DNA sequence specific and nonspecific. The crossover observed in real experiments is numerically recovered. We demonstrate that the evolution trajectories are drastically dispersed and no typical evolution passage exists during the evolution. Particularly, Fisher's theorem of natural selection is verified. A theoretical analysis for the evolution is also included.
authors.affiliation: Department of Physics, Peking University, 100871 Beijing, China.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Yang
authors.forename: Hongli
authors.initials: H
authors.lastname: Wang
authors.forename: Qi
authors.initials: Q
authors.lastname: Ouyang
mesh_terms: D004247:DNA / Q000737:chemistry*; D019143:Evolution, Molecular; D007700:Kinetics; D015233:Models, Statistical; D008962:Models, Theoretical; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012097:Repressor Proteins / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics; D014764:Viral Proteins / Q000737:chemistry* / Q000378:metabolism; D054334:Viral Regulatory and Accessory Proteins
chemical_list: D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D004247:DNA