title: DNA as a universal substrate for chemical kinetics.
abstract: Molecular programming aims to systematically engineer molecular and chemical systems of autonomous function and ever-increasing complexity. A key goal is to develop embedded control circuitry within a chemical system to direct molecular events. Here we show that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of arbitrary systems of coupled chemical reactions. By using strand displacement reactions as a primitive, we construct reaction cascades with effectively unimolecular and bimolecular kinetics. Our construction allows individual reactions to be coupled in arbitrary ways such that reactants can participate in multiple reactions simultaneously, reproducing the desired dynamical properties. Thus arbitrary systems of chemical equations can be compiled into real chemical systems. We illustrate our method on the Lotka-Volterra oscillator, a limit-cycle oscillator, a chaotic system, and systems implementing feedback digital logic and algorithmic behavior.
authors.affiliation: Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA. dsolov@caltech.edu
authors.forename: David
authors.initials: D
authors.lastname: Soloveichik
authors.forename: Georg
authors.initials: G
authors.lastname: Seelig
authors.forename: Erik
authors.initials: E
authors.lastname: Winfree
mesh_terms: D055592:Biophysical Phenomena; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D008954:Models, Biological; D017711:Nonlinear Dynamics; D013598:Systems Theory
chemical_list: D004247:DNA