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Published March 23, 2010 | Supplemental Material + Published
Journal Article Open

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.

Additional Information

© 2010 by the National Academy of Sciences. Edited by José N. Onuchic, University of California San Diego, La Jolla, CA, and approved January 29, 2010 (received for review August 18, 2009). Published online before print March 4, 2010. A preliminary version of this work appeared as ref. 52. We thank L. Cardelli, D. Dotty, L. Qian, D. Zhang, J. Schaeffer, and M. Magnasco for useful discussions. This work was supported by National Science Foundation Grants EMT-0728703 and CCF-0832824 and Human Frontier Science Program Award RGY0074/2006-C.D.S. D.S. was supported by the CIFellows project. G.S. was supported by the Swiss National Science Foundation and a Burroughs Wellcome Fund CASI award. Author contributions: D.S., G.S., and E.W. designed research, performed research, and wrote the paper.

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Published - Soloveichik2010p7436P_Natl_Acad_Sci_Usa.pdf

Supplemental Material - pnas.0909380107_SI.pdf

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