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DNA as a universal substrate for chemical kinetics

Soloveichik, David and Seelig, Georg and Winfree, Erik (2010) DNA as a universal substrate for chemical kinetics. Proceedings of the National Academy of Sciences of the United States of America, 107 (12). pp. 5393-5398. ISSN 0027-8424. PMCID PMC2851759. https://resolver.caltech.edu/CaltechAUTHORS:20100413-092145583

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1073/pnas.0909380107DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851759PubMed CentralArticle
https://resolver.caltech.edu/CaltechAUTHORS:20200812-121640271Related ItemBook Chapter
ORCID:
AuthorORCID
Soloveichik, David0000-0002-2585-4120
Winfree, Erik0000-0002-5899-7523
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.
Funders:
Funding AgencyGrant Number
NSFEMT-0728703
NSFCCF-0832824
Human Frontier Science Program RGY0074/2006-C
Swiss National Science Foundation (SNSF)UNSPECIFIED
CASIUNSPECIFIED
Subject Keywords:molecular programming; mass-action kinetics; strand displacement cascades; chemical reaction networks; nonlinear chemical dynamics
Issue or Number:12
PubMed Central ID:PMC2851759
Record Number:CaltechAUTHORS:20100413-092145583
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20100413-092145583
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:17951
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:30 Apr 2010 04:33
Last Modified:12 Aug 2020 19:18

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