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Design and operation of reconfigurable two-dimensional DNA molecular arrays

Nature Protocolsvolume 13pages23122329 (2018) | Download Citation

Abstract

Information relay and cascaded transformation are essential in biology and engineering. Imitation of such complex behaviors via synthetic molecular self-assembly at the nanoscale remains challenging. Here we describe the use of structural DNA nanotechnology to realize prescribed, multistep, long-range information relay and cascaded transformation in rationally designed molecular arrays. The engineered arrays provide a controlled platform for studying complex dynamic behaviors of molecular arrays and have a range of potential applications, such as with reconfigurable metamaterials. A reconfigurable array consists of a prescribed number of interconnected dynamic DNA antijunctions. Each antijunction unit consists of four DNA domains of equal length with four dynamic nicking points, which are capable of switching between two stable conformations through an intermediate open conformation. By interconnecting the small DNA antijunctions, one can build custom two-dimensional (2D) molecular ‘domino’ arrays with arbitrary shapes. More important, the DNA molecular arrays are capable of undergoing programmed, multistep, long-range transformation driven by information relay between neighboring antijunction units. The information relay is initiated by the trigger strands under high temperature or formamide concentration. The array’s dynamic behavior can be regulated by external factors such as its shape and size, points of transformation initiation, and/or any engineered information propagation pathways. This protocol provides detailed strategies for designing DNA molecular arrays, as well as procedures for sample production, purification, reconfiguration, and imaging by atomic force microscopy (AFM) and transmission electron microscopy (TEM). The procedure can be completed in 4–7 d.

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Additional information

Article describing the development of the approach

1. Song, J. et al. Science 357, eaan3377 (2017): https://doi.org/10.1126/science.aan3377

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Acknowledgements

This work was supported by the NSF (CAREER Award DMR-1654485), the Wallace H. Coulter Department of Biomedical Engineering Startup Fund, a Billi and Bernie Marcus Research Award (to Y.K.), the National Natural Scientific Foundation of China (grants 11761141006 and 21605102 to J.S.), and the National Key Research and Development Program of China (grant 2017FYA0205301 to D.C.).

Author information

Author notes

  1. These authors contributed equally: Dongfang Wang, Jie Song

Affiliations

  1. Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Centre for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China

    • Dongfang Wang
    • , Jie Song
    •  & Daxiang Cui
  2. Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA

    • Pengfei Wang
    • , Victor Pan
    •  & Yonggang Ke
  3. State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, China

    • Yingwei Zhang
  4. Department of Chemistry, Emory University, Atlanta, GA, USA

    • Yonggang Ke

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  2. Search for Jie Song in:

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Contributions

J.S. and Y.K. conceived and led the project. J.S., P.W., and Y.K. designed and conducted the experiments. D.W., J.S., P.W., V.P., Y.Z., D.C., and Y.K. contributed to the writing of the manuscript.

Competing interests

A provisional US patent application based on the work described in this paper has been filed.

Corresponding authors

Correspondence to Jie Song or Daxiang Cui or Yonggang Ke.

Integrated supplementary information

  1. Supplementary Figure 1

    Design diagram of the 11 × 4 52-bp DNA origami array.

  2. Supplementary Figure 2

    Design diagram of the 20 × 8 42-bp DNA brick array.

Supplementary information

  1. Supplementary Figures 1 and 2 and Supplementary Tables 1 and 2

  2. Reporting Summary

  3. Supplementary Data 1

    Python code for sequence generation

  4. Supplementary Data 2

    caDNAno files for the 11 × 4 52-bp DNA origami array and the 20 × 8 42-bp DNA brick array

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DOI

https://doi.org/10.1038/s41596-018-0039-0

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