David Soloveichik a,1, Georg Seelig a,b,1, and Erik Winfree c,1
-Author Affiliations
aDepartment of Computer Science and Engineering, University of Washington, Seattle, WA 98195;
bDepartment of Electrical Engineering, University of Washington, Seattle, WA 98195; and
cDepartments of Computer Science, Computation and Neural Systems, and Bioengineering, California Institute of Technology, Pasadena, CA 91125
A preliminary version of this work appeared as ref. 52.
Edited by José N. Onuchic, University of California San Diego, La Jolla, CA, and approved January 29, 2010 (received for review August 18, 2009)
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.
molecular programming mass-action kinetics strand displacement cascades chemical reaction networks
nonlinear chemical dynamics
Footnotes
1To whom correspondence may be addressed. E-mail: dsolov@caltech.edu,gseelig@u.washington.edu, or winfree@caltech.edu.
Author contributions: D.S., G.S., and E.W. designed research, performed research, and wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
This article contains supporting information online at www.pnas.org/cgi/content/full/0909380107/DCSupplemental.
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