Dynamic protein assembly by programmable DNA strand displacement

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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Fig. 1: Strand displacement-based protein–DNA device.
Fig. 2: Multi-input and reversible device architectures.
Fig. 3: Signal amplification protein–DNA device.
Fig. 4: Dynamic artificial cellulosome.
Fig. 5: miRNA input-guided prodrug activation device.

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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).

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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.

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Correspondence to Wilfred Chen.

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Chen, R.P., Blackstock, D., Sun, Q. et al. Dynamic protein assembly by programmable DNA strand displacement. Nature Chem 10, 474–481 (2018). https://doi.org/10.1038/s41557-018-0016-9

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