Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges

3D
polyhedral wireframe DNA nanoparticles (DNA-NPs) fabricated
using scaffolded DNA origami offer complete and independent control
over NP size, structure, and asymmetric functionalization on the 10–100
nm scale. However, the complex DNA sequence design needed for the
synthesis of these versatile DNA-NPs has limited their widespread
use to date. While the automated sequence design algorithms DAEDALUS
and vHelix-BSCOR apply to DNA-NPs synthesized using either uniformly
dual or hybrid single-dual duplex edges, respectively, these DNA-NPs
are relatively compliant mechanically and are therefore of limited
utility for some applications. Further, these algorithms are incapable
of handling DNA-NP edge designs composed of more than two duplexes,
which are needed to enhance DNA-NP mechanical stiffness. As an alternative,
here we introduce the scaffolded DNA origami sequence design algorithm
TALOS, which is a generalized procedure for the fully automated design
of wireframe 3D polyhedra composed of edges of any cross section with
an even number of duplexes, and apply it to DNA-NPs composed uniformly
of single honeycomb edges. We also introduce a multiway vertex design
that enables the fabrication of DNA-NPs with arbitrary edge lengths
and vertex angles and apply it to synthesize a highly asymmetric origami
object. Sequence designs are demonstrated to fold robustly into target
DNA-NP shapes with high folding efficiency and structural fidelity
that is verified using single particle cryo-electron microscopy
and 3D reconstruction. In order to test its generality, we apply TALOS
to design an in silico library of over 200 DNA-NPs
of distinct symmetries and sizes, and for broad impact, we also provide
the software as open source for the generation of custom NP designs.