title: Model-driven engineering of RNA devices to quantitatively program gene expression.
abstract: The models and simulation tools available to design functionally complex synthetic biological devices are very limited. We formulated a design-driven approach that used mechanistic modeling and kinetic RNA folding simulations to engineer RNA-regulated genetic devices that control gene expression. Ribozyme and metabolite-controlled, aptazyme-regulated expression devices with quantitatively predictable functions were assembled from components characterized in vitro, in vivo, and in silico. The models and design strategy were verified by constructing 28 Escherichia coli expression devices that gave excellent quantitative agreement between the predicted and measured gene expression levels (r = 0.94). These technologies were applied to engineer RNA-regulated controls in metabolic pathways. More broadly, we provide a framework for studying RNA functions and illustrate the potential for the use of biochemical and biophysical modeling to develop biological design methods.
authors.affiliation: California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley CA 94720, USA.
authors.forename: James M
authors.initials: JM
authors.lastname: Carothers
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Goler
authors.forename: Darmawi
authors.initials: D
authors.lastname: Juminaga
authors.forename: Jay D
authors.initials: JD
authors.lastname: Keasling
mesh_terms: D003198:Computer Simulation; D017076:Computer-Aided Design; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D005818:Genetic Engineering; D008024:Ligands; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008957:Models, Genetic; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D010649:Phenylalanine / Q000031:analogs & derivatives / Q000378:metabolism; D059370:RNA Folding; D016337:RNA, Catalytic / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D058615:Synthetic Biology; D013806:Theophylline / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D008024:Ligands; D016337:RNA, Catalytic; C009722:4-aminophenylalanine; D010649:Phenylalanine; D013806:Theophylline