Article | Published:

A spatially localized architecture for fast and modular DNA computing

Nature Nanotechnology volume 12, pages 920927 (2017) | Download Citation

Abstract

Cells use spatial constraints to control and accelerate the flow of information in enzyme cascades and signalling networks. Synthetic silicon-based circuitry similarly relies on spatial constraints to process information. Here, we show that spatial organization can be a similarly powerful design principle for overcoming limitations of speed and modularity in engineered molecular circuits. We create logic gates and signal transmission lines by spatially arranging reactive DNA hairpins on a DNA origami. Signal propagation is demonstrated across transmission lines of different lengths and orientations and logic gates are modularly combined into circuits that establish the universality of our approach. Because reactions preferentially occur between neighbours, identical DNA hairpins can be reused across circuits. Co-localization of circuit elements decreases computation time from hours to minutes compared to circuits with diffusible components. Detailed computational models enable predictive circuit design. We anticipate our approach will motivate using spatial constraints for future molecular control circuit designs.

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Acknowledgements

The authors thank K. Strauss and L. Ceze for their support in initiating this project and F. Randisi for assistance with oxDNA simulations. This work was supported by National Science Foundation grants CCF-1409831, CCF-1317653 and IIS-1212940 and Office of Naval Research grant N00014-13-1-0880 to G.S. G.C. was partially supported by Microsoft Research Ltd.

Author information

Affiliations

  1. Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA

    • Gourab Chatterjee
  2. Microsoft Research, Cambridge CB1 2FB, UK

    • Neil Dalchau
    •  & Andrew Phillips
  3. Department of Electrical Engineering, University of Washington, Seattle, Washington 98195, USA

    • Richard A. Muscat
    •  & Georg Seelig
  4. Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington 98195, USA

    • Georg Seelig

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Contributions

G.C., N.D., R.A.M., A.P. and G.S. designed the experiments and wrote the paper. G.C. performed the experiments. N.D. and A.P. performed the modelling studies.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Andrew Phillips or Georg Seelig.

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DOI

https://doi.org/10.1038/nnano.2017.127

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