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Updated: May 14, 2025

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
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Arbitrary Design of DNA-Programmable 3D Crystals through Symmetry Mapping.

Jason S Kahn1, Daniel C Redeker2, Aaron Michelson1

  • 1Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States.

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Summary

This study introduces a novel algorithm for designing complex 3D nanostructures using DNA self-assembly. The method simplifies design by minimizing DNA voxels, enabling precise nanoscale fabrication.

Keywords:
DNA nanotechnologyencoded assemblynanomaterialsnanoparticlesnanoscale inverse designself-assembly

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Area of Science:

  • Nanotechnology
  • Materials Science
  • Biotechnology

Background:

  • Nanoscale self-assembly enables intricate structure creation beyond traditional nanofabrication limits.
  • DNA nanotechnology offers programmability but faces challenges in designing complex 3D superlattices due to interaction complexity.
  • Streamlining assembly and component fabrication requires modular design strategies and reduced interaction complexity.

Purpose of the Study:

  • To propose a symmetry-mapping bond assignment algorithm for designing arbitrary 3D lattices from voxels.
  • To minimize the number of DNA-based voxels and reduce assembly information requirements.
  • To develop a scalable inverse design approach for programming bottom-up nanomaterial fabrication.

Main Methods:

  • Developed a symmetry-mapping bond assignment algorithm for designing 3D lattices.
  • Incorporated experimentally relevant DNA binding rules and restrictions.
  • Created software (MOSES) for Mapping Of Structurally Encoded aSsembly.
  • Demonstrated the algorithm with zinc blende, cubic Laves phase, and custom 'H' lattices.

Main Results:

  • The algorithm successfully guides the design of prescribed 3D lattices from voxels with directional, addressable bonds.
  • Demonstrated capability in assembling nanoscale analogs of known structures (ZnS, MgCu2) and novel motifs.
  • Minimized the complexity and number of DNA-based voxels required for assembly.
  • Provided a scalable inverse design solution for complex 3D nanostructures.

Conclusions:

  • The proposed algorithm offers a scalable solution for designing complex 3D nanostructures via DNA self-assembly.
  • This inverse design approach facilitates programming bottom-up nanomaterial fabrication.
  • The method enables the creation of nanostructures capable of carrying nanocargo.