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A Spatially Localized Architecture for Fast and Modular Computation at the Molecular Scale

Gourab Chatterjee, Neil Dalchau, Richard A. Muscat, Andrew Phillips, Georg Seelig
doi: https://doi.org/10.1101/110965
Gourab Chatterjee
1Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
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Neil Dalchau
2Microsoft Research, Cambridge CB1 2FB, UK
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Richard A. Muscat
3Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA
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Andrew Phillips
2Microsoft Research, Cambridge CB1 2FB, UK
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  • For correspondence: gseelig@uw.edu andrew.phillips@microsoft.com
Georg Seelig
3Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA
4Department of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
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  • For correspondence: gseelig@uw.edu andrew.phillips@microsoft.com
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Abstract

Cells use spatial constraints to control and accelerate the flow of information in enzyme cascades and signaling networks. 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 neighbors, identical DNA hairpins can be reused across circuits. Colocalization 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 that our approach will motivate the use of spatial constraints in molecular engineering more broadly, bringing embedded molecular control circuits closer to applications.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 23, 2017.
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A Spatially Localized Architecture for Fast and Modular Computation at the Molecular Scale
Gourab Chatterjee, Neil Dalchau, Richard A. Muscat, Andrew Phillips, Georg Seelig
bioRxiv 110965; doi: https://doi.org/10.1101/110965
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A Spatially Localized Architecture for Fast and Modular Computation at the Molecular Scale
Gourab Chatterjee, Neil Dalchau, Richard A. Muscat, Andrew Phillips, Georg Seelig
bioRxiv 110965; doi: https://doi.org/10.1101/110965

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