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Computing in mammalian cells with nucleic acid strand exchange

Nature Nanotechnology volume 11, pages 287–294 (2016)Cite this article

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Abstract

DNA strand displacement has been widely used for the design of molecular circuits, motors, and sensors in cell-free settings. Recently, it has been shown that this technology can also operate in biological environments, but capabilities remain limited. Here, we look to adapt strand displacement and exchange reactions to mammalian cells and report DNA circuitry that can directly interact with a native mRNA. We began by optimizing the cellular performance of fluorescent reporters based on four-way strand exchange reactions and identified robust design principles by systematically varying the molecular structure, chemistry and delivery method. Next, we developed and tested AND and OR logic gates based on four-way strand exchange, demonstrating the feasibility of multi-input logic. Finally, we established that functional siRNA could be activated through strand exchange, and used native mRNA as programmable scaffolds for co-localizing gates and visualizing their operation with subcellular resolution.

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Figure 1: Empirical design parameters determine in-cell performance.
Figure 2: Strand exchange reactions work in mammalian cells.
Figure 3: Strand exchange-based OR and AND logic gates work in mammalian cells.
Figure 4: A functional siRNA can be activated through four-way strand exchange.
Figure 5: Endogenous mRNA and mMTRIPS can serve as scaffolds for strand exchange reactions.
Figure 6: ACTB mRNA-scaffolded mMTRIP AND logic gates work in cells.

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Acknowledgements

We thank D. Soloveichik, E. Winfree, and D. Y. Zhang for their help in designing the logic AND gate. This material is based on work supported by the Defense Advanced Research Projects Agency (DARPA) under Contract No. W911NF-11-2-0068 to G.S. and P.J.S. Additional support was provided by NSF CAREER Award No. 1253691 (P.J.S.), regarding RNA imaging, and NIH GM094198 (P.J.S.), for the use of hRSV cell models during development.

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Author notes

  1. Benjamin Groves, Yuan-Jyue Chen and Chiara Zurla: These authors contributed equally to this work

Authors and Affiliations

  1. Department of Electrical Engineering, University of Washington, Seattle, Washington, USA

    Benjamin Groves, Yuan-Jyue Chen, Sergii Pochekailov & Georg Seelig

  2. Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, USA

    Chiara Zurla, Jonathan L. Kirschman & Philip J. Santangelo

  3. Department of Computer Science & Engineering, University of Washington, Seattle, Washington, USA

    Georg Seelig

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Contributions

P.J.S. and G.S. conceived the project, B.G., Y.-J.C., C.Z., S.P., P.J.S. and G.S. designed experiments, B.G., Y.-J.C., C.Z., and S.P. performed the experiments, J.L.K. and P.S. developed the monovalent MTRIPs, B.G., Y.-J.C., C.Z., analysed the data, B.G. Y.-J. C., C.Z., P.J.S, and G.S. wrote the paper.

Corresponding authors

Correspondence to Philip J. Santangelo or Georg Seelig.

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The authors declare no competing financial interests.

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Groves, B., Chen, YJ., Zurla, C. et al. Computing in mammalian cells with nucleic acid strand exchange. Nature Nanotech 11, 287–294 (2016). https://doi.org/10.1038/nnano.2015.278

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