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Self-replication of DNA rings

Nature Nanotechnology volume 10, pages 528–533 (2015)Cite this article

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Abstract

Biology provides numerous examples of self-replicating machines, but artificially engineering such complex systems remains a formidable challenge. In particular, although simple artificial self-replicating systems including wooden blocks1,2, magnetic systems3,4, modular robots5,6 and synthetic molecular systems7,8,9 have been devised, such kinematic self-replicators10 are rare compared with examples of theoretical cellular self-replication11,12,13,14,15,16,17,18. One of the principal reasons for this is the amount of complexity that arises when you try to incorporate self-replication into a physical medium19. In this regard, DNA is a prime candidate material for constructing self-replicating systems due to its ability to self-assemble through molecular recognition20. Here, we show that DNA T-motifs, which self-assemble into ring structures21,22, can be designed to self-replicate through toehold-mediated strand displacement reactions23,24. The inherent design of these rings allows the population dynamics of the systems to be controlled. We also analyse the replication scheme within a universal framework of self-replication25 and derive a quantitative metric of the self-replicability of the rings.

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Figure 1: The replicating entities.
Figure 2: Replication mechanism and pathways.
Figure 3: Population dynamics of the two types of replication scheme and AFM images of each phase.
Figure 4: Population growth and self-replicability calculations.

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Acknowledgements

The authors thank J. Kim and A. Tandon for discussions and technical assistance with DNA extraction. S.H.P. was supported by the National Research Foundation of Korea (grants 2012R1A2A2A01005985, 2014R1A2A1A11053213 and 2012M3A7B4049801), funded by the Korean government (Ministry of Science, ICT and Future Planning and Ministry of Education). S.M. and S.H. were supported by Grant-in-aid for Scientific Research grants (nos. 22220001/24104005 and 23800006/24104005, respectively) from the Japanese government (Ministry of Education, Culture, Sports, Science and Technology).

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Author notes

  1. Shogo Hamada

    Present address: Present address: Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, USA,

Authors and Affiliations

  1. Department of Physics, Sungkyunkwan University, Suwon, 440-746, Korea

    Junghoon Kim & Sung Ha Park

  2. Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 440-746, Korea

    Junwye Lee & Sung Ha Park

  3. Department of Bioengineering and Robotics, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Miyagi, Japan

    Shogo Hamada & Satoshi Murata

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  1. Junghoon Kim
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Contributions

J.K. initiated and directed the project, designed experiments, performed the experiments, carried out the theoretical modelling and calculations, and analysed data and wrote the paper (with input from others). J.L. analysed data and wrote the paper. S.H. analysed data and wrote the paper. S.M. analysed data and wrote the paper. S.H.P. initiated and directed the project, designed experiments, analysed data and wrote the paper.

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Correspondence to Sung Ha Park.

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Kim, J., Lee, J., Hamada, S. et al. Self-replication of DNA rings. Nature Nanotech 10, 528–533 (2015). https://doi.org/10.1038/nnano.2015.87

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