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Dynamic protein assembly by programmable DNA strand displacement

Nature Chemistryvolume 10pages474481 (2018) | Download Citation

Abstract

Inspired by the remarkable ability of natural protein switches to sense and respond to a wide range of environmental queues, here we report a strategy to engineer synthetic protein switches by using DNA strand displacement to dynamically organize proteins with highly diverse and complex logic gate architectures. We show that DNA strand displacement can be used to dynamically control the spatial proximity and the corresponding fluorescence resonance energy transfer between two fluorescent proteins. Performing Boolean logic operations enabled the explicit control of protein proximity using multi-input, reversible and amplification architectures. We further demonstrate the power of this technology beyond sensing by achieving dynamic control of an enzyme cascade. Finally, we establish the utility of the approach as a synthetic computing platform that drives the dynamic reconstitution of a split enzyme for targeted prodrug activation based on the sensing of cancer-specific miRNAs.

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Acknowledgements

We thank S. Michnick for providing the split yCD constructs. This work was supported by grants from National Science Foundation (CBET1510817 and MCB1543838).

Author information

Author notes

  1. These authors contributed equally: Rebecca P. Chen and Daniel Blackstock.

Affiliations

  1. Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA

    • Rebecca P. Chen
    • , Daniel Blackstock
    • , Qing Sun
    •  & Wilfred Chen

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Contributions

R.P.C., D.B. and W.C. conceived the project. R.P.C., D.B., Q.S. and W.C. designed experiments. R.P.C. and D.B. performed the FRET experiments. R.P.C. and Q.S. performed the enzyme cascade experiments. R.P.C. performed the split yCD experiments. R.P.C., D.B., Q.S. and W.C. analysed the data. R.P.C., D.B., Q.S. and W.C. wrote the paper. All authors discussed the results and commented on the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Wilfred Chen.

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DOI

https://doi.org/10.1038/s41557-018-0016-9