Arbitrary Design of DNA-Programmable 3D Crystals through Symmetry Mapping

Nanoscale self-assembly
offers exciting potential for
creating
intricate structures beyond the limits of traditional top-down nanofabrication.
Despite advancements in molecularly programmable assembly, particularly
utilizing DNA nanotechnology, challenges remain in defining precise
assembly instructions for the formation of complex three-dimensional
(3D) superlattice architectures. DNA-based self-assembly methods offer
programmability through sequence-encoded addressable bonds, but the
difficulty lies in reducing the complexity and number of these interactions
to establish a modular, structural design strategy and streamline
the assembly and component fabrication process. This work proposes
a symmetry-mapping bond assignment algorithm to guide the design of
arbitrarily prescribed 3D lattices self-assembled from voxels with
directional, addressable bonds and capable of carrying nanocargo.
The algorithm enables the minimization of the number of DNA-based
voxels, thus reducing the amount of information required to encode
assembly. The developed approach leverages the symmetries of the target
lattices, assembled from voxels, but significantly incorporates experimentally
relevant binding rules and restrictions specific to DNA-based systems.
We discuss the developed algorithm and demonstrate its capability
in selected examples of nanoscale analogs of zinc blende (ZnS) and
cubic Laves phase (MgCu2), as well as a lattice based on
an arbitrarily designed motif (letter H). Through the established
algorithm and associated software for Mapping Of Structurally Encoded
aSsembly (MOSES), this inverse design approach provides a scalable
solution for designing complexly organized 3D nanostructures, providing
a means for programming bottom-up nanomaterial fabrication.