Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.
Subscribe

Logo for

Science 318 (5853): 1121-1125

Copyright © 2007 by the American Association for the Advancement of Science

Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA

David Yu Zhang,1{dagger} Andrew J. Turberfield,2 Bernard Yurke,3* Erik Winfree1{dagger}

Abstract: Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics.

1 Computation and Neural Systems, California Institute of Technology, MC 136-93, 1200 East California Boulevard, Pasadena, CA91125, USA.
2 Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, UK.
3 Bell Laboratories, Alcatel-Lucent, Murray Hill, NJ 07974, USA.

* Present address: Materials Science and Engineering Department, Boise State University, Boise, ID 83725, USA.

{dagger} To whom correspondence should be addressed. E-mail: winfree{at}caltech.edu (E.W.); dzhang{at}dna.caltech.edu (D.Y.Z.)

THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Stacking nonenzymatic circuits for high signal gain.
X. Chen, N. Briggs, J. R. McLain, and A. D. Ellington (2013)
PNAS 110, 5386-5391
   Abstract »    Full Text »    PDF »
Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions.
H. Chandran, N. Gopalkrishnan, B. Yurke, and J. Reif (2012)
J R Soc Interface 9, 1637-1653
   Abstract »    Full Text »    PDF »
Configuring robust DNA strand displacement reactions for in situ molecular analyses.
D. Y. Duose, R. M. Schweller, J. Zimak, A. R. Rogers, W. N. Hittelman, and M. R. Diehl (2012)
Nucleic Acids Res. 40, 3289-3298
   Abstract »    Full Text »    PDF »
Abstractions for DNA circuit design.
M. R. Lakin, S. Youssef, L. Cardelli, and A. Phillips (2012)
J R Soc Interface 9, 470-486
   Abstract »    Full Text »    PDF »
Aptameric Molecular Switch for Cascade Signal Amplification.
C. Ma, C. Zhao, Y. Ge, and C. Shi (2012)
Clin. Chem. 58, 384-390
   Abstract »    Full Text »    PDF »
A simple DNA gate motif for synthesizing large-scale circuits.
L. Qian and E. Winfree (2011)
J R Soc Interface 8, 1281-1297
   Abstract »    Full Text »    PDF »
Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods.
B. Li, A. D. Ellington, and X. Chen (2011)
Nucleic Acids Res. 39, e110
   Abstract »    Full Text »    PDF »
Scaling Up DNA Computation.
J. H. Reif (2011)
Science 332, 1156-1157
   Abstract »    Full Text »    PDF »
Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades.
L. Qian and E. Winfree (2011)
Science 332, 1196-1201
   Abstract »    Full Text »    PDF »
Robustness and modularity properties of a non-covalent DNA catalytic reaction.
D. Y. Zhang and E. Winfree (2010)
Nucleic Acids Res. 38, 4182-4197
   Abstract »    Full Text »    PDF »
Strategies for protein synthetic biology.
R. Grunberg and L. Serrano (2010)
Nucleic Acids Res. 38, 2663-2675
   Abstract »    Full Text »    PDF »
DNA as a universal substrate for chemical kinetics.
D. Soloveichik, G. Seelig, and E. Winfree (2010)
PNAS 107, 5393-5398
   Abstract »    Full Text »    PDF »
Modelling amorphous computations with transcription networks.
Z. B. Simpson, T. L. Tsai, N. Nguyen, X. Chen, and A. D. Ellington (2009)
J R Soc Interface 6, S523-S533
   Abstract »    Full Text »    PDF »
A programming language for composable DNA circuits.
A. Phillips and L. Cardelli (2009)
J R Soc Interface 6, S419-S436
   Abstract »    Full Text »    PDF »
MATERIALS SCIENCE: DNA Circuits Get Up to Speed.
R. Bar-Ziv (2007)
Science 318, 1078-1079
   Abstract »    Full Text »    PDF »

To Advertise     Find Products

Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882