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Exponential growth and selection in self-replicating materials from DNA origami rafts

Abstract

Self-replication and evolution under selective pressure are inherent phenomena in life, and but few artificial systems exhibit these phenomena1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17. We have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temperature and ultraviolet illumination, producing more than 7 million copies in 24 cycles. We demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. In one species, pH-sensitive triplex DNA bonds enable parent–daughter templating, while in the second species, triplex binding inhibits the formation of duplex DNA templating. At pH 5.3, the replication rate of species I is 1.3–1.4 times faster than that of species II. At pH 7.8, the replication rates are reversed. When mixed together in the same vial, the progeny of species I replicate preferentially at pH 7.8; similarly at pH 5.3, the progeny of species II take over the system. This addressable selectivity should be adaptable to the selection and evolution of multi-component self-replicating materials in the nanoscopic-to-microscopic size range.

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Figure 1: DNA origami raft design and self-replication cycling.
Figure 2: Self-replication of DNA seeds.
Figure 3: Self-replication controlled by intra- and inter-molecular DNA triplex.
Figure 4: Self-replication enabling selection.

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Acknowledgements

We would like to acknowledge W. Liu, D. Niu and Y. Zhang for useful discussions. This research has been supported primarily by DOE DE-SC0007991 (PMC, NCS) for initiation, design, analysis and imaging, and partially by grant GBMF3849 from the Gordon and Betty Moore Foundation (PMC, NCS) for origami preparation and characterization, GM-29554 from NIGMS, grants CMMI-1120890 and CCF-1117210 from the NSF, MURI W911NF-11-1-0024 from ARO, grants N000141110729 and N000140911118 from ONR (NCS) for sequence design, DNA synthesis, purification and characterization. Y.M. and X.H. acknowledge the support by the Earmarked Grant from the University Grant Council of the Hong Kong Government, RGC 16302415, and the China 985 Grant of Tongji University. X.H. was supported partially by the MRSEC Program of the National Science Foundation under Award Number DMR-1420073 for pH-sensitive sequence design and characterization. We also wish to acknowledge the support of the National Science Foundation Academic Research Infrastructure program through Award No. CMMI-0957834.

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X.H., R.S., N.C.S. and P.M.C. designed the experiments. X.H., R.S. and R.Z. performed the experiments, and all of the authors analysed data and wrote the manuscript.

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Correspondence to Paul M. Chaikin or Nadrian C. Seeman.

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The authors declare no competing financial interests.

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He, X., Sha, R., Zhuo, R. et al. Exponential growth and selection in self-replicating materials from DNA origami rafts. Nature Mater 16, 993–997 (2017). https://doi.org/10.1038/nmat4986

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