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Solving mazes with single-molecule DNA navigators

Nature Materials volume 18, pages 273–279 (2019)Cite this article

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Abstract

Molecular devices with information-processing capabilities hold great promise for developing intelligent nanorobotics. Here we demonstrate a DNA navigator system that can perform single-molecule parallel depth-first search on a ten-vertex rooted tree defined on a two-dimensional DNA origami platform. Pathfinding by the DNA navigators exploits a localized strand exchange cascade, which is initiated at a unique trigger site on the origami with subsequent automatic progression along paths defined by DNA hairpins containing a universal traversal sequence. Each single-molecule navigator autonomously explores one of the possible paths through the tree. A specific solution path connecting a given pair of start and end vertices can then be easily extracted from the set of all paths taken by the navigators collectively. The solution path laid out on origami is illustrated with single-molecule imaging. Our approach points towards the realization of molecular materials with embedded computational functions operating at the single-molecule level.

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Fig. 1: Physical implementation of the single-molecule DNA navigator.
Fig. 2: Single-molecule characterization of kinetics of PSEC.
Fig. 3: PSEC-driven graph traversal on a maze.
Fig. 4: Single-molecule DNA navigators for maze-solving.

Data availability

All the data that support the findings of this study are available within the paper and its Supplementary Information files, and from the corresponding authors upon reasonable request. 

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Acknowledgements

We greatly appreciate financial support from the Ministry of Science and Technology of China (2016YFA0201200), National Science Foundation of China (21390414, 21473236, 21675167, 21505148, 21722310, 61771253), and the Chinese Academy of Sciences (QYZDJ-SSW-SLH031). We further acknowledge support by the Deutsche Forschungsgemeinschaft through SFB1032 Project A2 and by the Technical University Munich International Graduate School
of Science and Engineering.

Author information

Author notes

  1. These authors contributed equally: Jie Chao, Jianbang Wang, Fei Wang and Xiangyuan Ouyang.

Authors and Affiliations

  1. Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, China

    Jie Chao, Lianhui Wang & Wei Huang

  2. Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China

    Jie Chao, Jianbang Wang, Xiangyuan Ouyang, Huajie Liu, Jiye Shi, Lihua Wang, Jun Hu & Chunhai Fan

  3. School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China

    Fei Wang, Qian Li & Chunhai Fan

  4. Joint Research Center for Precision Medicine, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital South Campus, Shanghai Fengxian Central Hospital, Shanghai, China

    Fei Wang

  5. Physics of Synthetic Biological Systems (E14), Physics Department, Technische Universität München, Garching, Germany

    Enzo Kopperger & Friedrich C. Simmel

  6. School of Chemical Science and Engineering, Tongji Univeristy, Shanghai, China

    Huajie Liu

  7. Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China

    Lihua Wang

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  1. Jie Chao
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Contributions

C.F. directed the research. C.F., F.C.S., H.L. and J.C. conceived the project and designed the experiments. J.C., J.W., F.W., X.O. and E.K. designed the DNA sequences, constructed the navigator system and performed the single-molecule studies. F.W., Q.L. and J.S. carried out the theoretical simulation. J.C., J.W., F.W., E.K., H.L., Lihua W., J.H., Lianhui W., W.H. and F.C.S. analysed the data. All authors discussed the results and commented on the manuscript. C.F., F.C.S. and H.L. co-wrote the paper.

Corresponding authors

Correspondence to Huajie Liu, Friedrich C. Simmel or Chunhai Fan.

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The authors declare no competing interests.

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Supplementary Information

Supplementary Notes 1–4, Supplementary Schemes 1–3, Supplementary Software, Supplementary Figures 1–26, Supplementary References 1–3

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Chao, J., Wang, J., Wang, F. et al. Solving mazes with single-molecule DNA navigators. Nature Mater 18, 273–279 (2019). https://doi.org/10.1038/s41563-018-0205-3

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