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Pattern transformation with DNA circuits

Nature Chemistry volume 5, pages 1000–1005 (2013)Cite this article

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Abstract

Readily programmable chemical networks are important tools as the scope of chemistry expands from individual molecules to larger molecular systems. Although many complex systems are constructed using conventional organic and inorganic chemistry, the programmability of biological molecules such as nucleic acids allows for precise, high-throughput and automated design, as well as simple, rapid and robust implementation. Here we show that systematic and quantitative control over the diffusivity and reactivity of DNA molecules yields highly programmable chemical reaction networks (CRNs) that execute at the macroscale. In particular, we designed and implemented non-enzymatic DNA circuits capable of performing pattern-transformation algorithms such as edge detection. We also showed that it is possible to fine-tune and multiplex such circuits. We believe these strategies will provide programmable platforms on which to prototype CRNs, discover bottom-up construction principles and generate patterns in materials.

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Figure 1: High-level description and molecular detail of an incoherent feed-forward loop that performs edge detection.
Figure 2: Execution of the incoherent feed-forward loop that performs edge detection.
Figure 3: High-level description and molecular detail of the ‘positive edge’ circuit.
Figure 4: Execution of the ‘positive edge’ and ‘edge splitter’ circuits.
Figure 5: Combinatorial multiplexing of two-channel pattern-transformation programs.

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Acknowledgements

This work was supported by the National Institute of Health (NIH) (R01GM094933) and a National Security Science and Engineering Faculty Fellowship (FA9550-10-1-0169). P.B.A. was supported by an NIH National Research Service Award Fellowship (1 F32 GM095280). X.C. was partially supported by a postdoctoral trainee fellowship from the Cancer Prevention Research Institute of Texas. We thank S. N. Adai for assistance with editing.

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Author notes

  1. Xi Chen

    Present address: Present address: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA,

Authors and Affiliations

  1. Department of Biomedical Engineering, University of Texas at Austin, Austin, 78712, Texas, USA

    Steven M. Chirieleison

  2. Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, 78712, Texas, USA

    Peter B. Allen, Zack B. Simpson, Andrew D. Ellington & Xi Chen

  3. Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, 78712, Texas, USA

    Andrew D. Ellington & Xi Chen

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  1. Steven M. Chirieleison
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Contributions

S.M.C. designed sequences for several circuits and performed the majority of the experiments. Z.B.S. and P.B.A. performed computer simulations. A.D.E. supervised the project and designed diffusion-programming tests and some quantitative analyses. X.C. conceived the project, designed most circuits and performed pilot experiments. S.M.C., X.C., P.B.A. and A.D.E. wrote the manuscript.

Corresponding authors

Correspondence to Andrew D. Ellington or Xi Chen.

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The authors declare no competing financial interests.

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Chirieleison, S., Allen, P., Simpson, Z. et al. Pattern transformation with DNA circuits. Nature Chem 5, 1000–1005 (2013). https://doi.org/10.1038/nchem.1764

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