Dynamic DNA-toolbox reaction circuits: a walkthrough.
In living organisms, the integration of signals from the environment and the molecular computing leading to a cellular response are orchestrated by Gene Regulatory Networks (GRN). However, the molecular complexity of in vivo genetic regulation makes it next to impossible to describe in a quantitative manner. Reproducing, in vitro, reaction networks that could mimic the architecture and behavior of in vivo networks, yet lend themselves to mathematical modeling, represents a useful strategy to understand, and even predict, the function of GRN. In this paper, we define a set of in vitro, DNA-based molecular transformations that can be linked to each other in such a way that the product of one transformation can activate or inhibit the production of one or several other DNA compounds. Therefore, these reactions can be wired in arbitrary networks. This approach provides an experimental way to reproduce the dynamic features of genetic regulation in a test tube. We introduce the rules to design the necessary DNA species, a guide to implement the chemical reactions and ways to optimize the experimental conditions. We finally show how this framework, or "DNA toolbox", can be used to generate an inversion module, though many other behaviors, including oscillators and bistable switches, can be implemented.
LIMMS/CNRS UMI2820 Institute of Industrial Science, The University of Tokyo, Komaba 4-6-1, Meguro-ku, Tokyo 155-0085, Japan; Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601 Université Paris Descartes, 45 rue des Saints Pères, 75006 Paris, France.
Alexandre
A
Baccouche
Graduate School of Medicine, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address: montagne@m.u-tokyo.ac.jp.
Kevin
K
Montagne
LIMMS/CNRS UMI2820 Institute of Industrial Science, The University of Tokyo, Komaba 4-6-1, Meguro-ku, Tokyo 155-0085, Japan.
Adrien
A
Padirac
LIMMS/CNRS UMI2820 Institute of Industrial Science, The University of Tokyo, Komaba 4-6-1, Meguro-ku, Tokyo 155-0085, Japan.
Teruo
T
Fujii
LIMMS/CNRS UMI2820 Institute of Industrial Science, The University of Tokyo, Komaba 4-6-1, Meguro-ku, Tokyo 155-0085, Japan. Electronic address: rondelez@iis.u-tokyo.ac.jp.
Yannick
Y
Rondelez
D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics; D025461:Feedback, Physiological; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D021141:Nucleic Acid Amplification Techniques; D054735:Phosphorothioate Oligonucleotides / Q000737:chemistry / Q000235:genetics
D054735:Phosphorothioate Oligonucleotides; D004247:DNA
Chemical oscillators; DNA toolbox; Enzymatic circuit; Molecular programming; Reaction networks