DNA as a Universal Substrate for Chemical Kinetics
In chemistry and biology, the formalism of mass action equations is commonly used to model and understand the time evolution of complex molecular systems. In a typical application we are given a system of interacting molecules and then try to build a chemical reaction model based on that knowledge. In this paper, we take the opposite approach and ask, "Given a formal chemical reaction network (CRN) with a desired dynamical behavior, can we find molecules that implement this behavior?" We argue that this is in fact possible, and propose a specific DNA-based implementation for arbitrary CRN. In our approach, the formalism of CRNs becomes a prescriptive "programming language" rather than a descriptive modeling language.
As one anonymous reviewer explained: “[This work] sets on a proper foundation the hundreds – perhaps thousands – of papers that have been published on the dynamics of CRNs... [T]here have been many instances where new mathematics and new design ideas were recognized as interesting, but were also criticized on the grounds that they were vapid: ‘How do you know that chemical reactions with these properties even exist?’ This paper proves that every chemical reaction network exists.”
An article published in the March issue of PNAS shows that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of arbitrary systems of coupled chemical reactions.