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Engineering Organization of DNA Nano-Chambers through Dimensionally Controlled and Multi-Sequence Encoded Differentiated Bonds

  • Zhiwei Lin
    Zhiwei Lin
    Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
    More by Zhiwei Lin
  • Hamed Emamy
    Hamed Emamy
    Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
    More by Hamed Emamy
  • Brian Minevich
    Brian Minevich
    Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
  • Yan Xiong
    Yan Xiong
    Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
    More by Yan Xiong
  • Shuting Xiang
    Shuting Xiang
    Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
  • Sanat Kumar
    Sanat Kumar
    Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
    More by Sanat Kumar
  • Yonggang Ke
    Yonggang Ke
    Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
    More by Yonggang Ke
  • , and 
  • Oleg Gang*
    Oleg Gang
    Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
    Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
    Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
    *[email protected]
    More by Oleg Gang
Cite this: J. Am. Chem. Soc. 2020, 142, 41, 17531–17542
Publication Date (Web):September 9, 2020
https://doi.org/10.1021/jacs.0c07263
Copyright © 2020 American Chemical Society

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    Abstract

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    Engineering the assembly of nanoscale objects into complex and prescribed structures requires control over their binding properties. Such control might benefit from a well-defined bond directionality, the ability to designate their engagements through specific encodings, and the capability to coordinate local orientations. Although much progress has been achieved in our ability to design complex nano-objects, the challenges in creating such nano-objects with fully controlled binding modes and understanding their fundamental properties are still outstanding. Here, we report a facile strategy for creating a DNA nanochamber (DNC), a hollow cuboid nano-object, whose bonds can be fully prescribed and complexly encoded along its three orthogonal axes, giving rise to addressable and differentiated bonds. The DNC can host nanoscale cargoes, which allows for the integration with functional nano-objects and their organization in larger-scale systems. We explore the relationship between the design of differentiated bonds and a formation of one-(1D), two-(2D), and three-(3D) dimensional organized arrays. Through the realization of different binding modes, we demonstrate sequence encoded nanoscale heteropolymers, helical polymers, 2D lattices, and mesoscale 3D nanostructures with internal order, and show that this assembly strategy can be applied for the organization of nanoparticles. We combine experimental investigations with computational simulation to understand the mechanism of structural formation for different types of ordered arrays, and to correlate the bonds design with assembly processes.

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    • Design and fabrication of DNA nanochamber, detailed experiment, modeling, and simulation description; and additional results and discussion (PDF)

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