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Programmable single-cell mammalian biocomputers

Abstract

Synthetic biology has advanced the design of standardized control devices that program cellular functions and metabolic activities in living organisms1. Rational interconnection of these synthetic switches resulted in increasingly complex designer networks that execute input-triggered genetic instructions with precision, robustness and computational logic reminiscent of electronic circuits2,3. Using trigger-controlled transcription factors, which independently control gene expression4,5, and RNA-binding proteins that inhibit the translation of transcripts harbouring specific RNA target motifs6,7, we have designed a set of synthetic transcription–translation control devices that could be rewired in a plug-and-play manner. Here we show that these combinatorial circuits integrated a two-molecule input and performed digital computations with NOT, AND, NAND and N-IMPLY expression logic in single mammalian cells. Functional interconnection of two N-IMPLY variants resulted in bitwise intracellular XOR operations, and a combinatorial arrangement of three logic gates enabled independent cells to perform programmable half-subtractor and half-adder calculations. Individual mammalian cells capable of executing basic molecular arithmetic functions isolated or coordinated to metabolic activities in a predictable, precise and robust manner may provide new treatment strategies and bio-electronic interfaces in future gene-based and cell-based therapies.

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Figure 1: Genetic switchboard of the biocomputer circuitry.
Figure 2: Design and processing performance of synthetic N-IMPLY gates in human cells.
Figure 3: Design and computation characteristics of the synthetic mammalian XOR processor.
Figure 4: Input-programmable half-subtractor and half-adder operations.

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Acknowledgements

We thank R. Singer for providing pMS2dIFG, M. Tigges for generous advice, E. Gutzwiller for experimental support, and M. Dessing and V. Jäggin for assistance with flow cytometry. This work was supported by the Swiss National Science Foundation (grant no. 31003A-126022) and in part by EC Framework 7 (Persist).

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Contributions

S.A., D.A., M.M., M.W. and M.F. designed the project, analysed results and wrote the manuscript. S.A., D.A. and M.M. performed the experimental work.

Corresponding author

Correspondence to Martin Fussenegger.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-11, Extended Figure legends for Figures 1-4 in the main paper and Supplementary Tables 1-2. (PDF 6932 kb)

Supplementary Movie 1

This movie file shows a time-lapse fluorescence microscopy of entire cell populations transfected with half-subtractor components programmed using different combinations of input signals (recorded for 75h; 1 frame/ 5 minutes; see also Fig. S7. (MP4 3231 kb)

Supplementary Movie 2

This movie file shows a time-lapse fluorescence microscopy of entire cell populations transfected with half-adder components programmed using different combinations of input signals (recorded for 75h; 1 frame/ 5 minutes; see also Fig. S7. (MP4 3134 kb)

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Ausländer, S., Ausländer, D., Müller, M. et al. Programmable single-cell mammalian biocomputers. Nature 487, 123–127 (2012). https://doi.org/10.1038/nature11149

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