title: Boosting functionality of synthetic DNA circuits with tailored deactivation.
abstract: Molecular programming takes advantage of synthetic nucleic acid biochemistry to assemble networks of reactions, in vitro, with the double goal of better understanding cellular regulation and providing information-processing capabilities to man-made chemical systems. The function of molecular circuits is deeply related to their topological structure, but dynamical features (rate laws) also play a critical role. Here we introduce a mechanism to tune the nonlinearities associated with individual nodes of a synthetic network. This mechanism is based on programming deactivation laws using dedicated saturable pathways. We demonstrate this approach through the conversion of a single-node homoeostatic network into a bistable and reversible switch. Furthermore, we prove its generality by adding new functions to the library of reported man-made molecular devices: a system with three addressable bits of memory, and the first DNA-encoded excitable circuit. Specific saturable deactivation pathways thus greatly enrich the functional capability of a given circuit topology.
authors.affiliation: Department of Mechanical Engineering, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Kevin
authors.initials: K
authors.lastname: Montagne
authors.affiliation: LIMMS/CNRS-IIS (UMI 2820), Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Gines
authors.affiliation: LIMMS/CNRS-IIS (UMI 2820), Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.
authors.forename: Teruo
authors.initials: T
authors.lastname: Fujii
authors.affiliation: LIMMS/CNRS-IIS (UMI 2820), Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.|Gulliver UMR7083 CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75010 Paris, France.
authors.forename: Yannick
authors.initials: Y
authors.lastname: Rondelez
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D025461:Feedback, Physiological; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry / Q000235:genetics
chemical_list: D009841:Oligonucleotides; D004247:DNA