Automated sequence design of 2D wireframe DNA origami with honeycomb edges

Abstract

Wireframe DNA origami has emerged as a powerful approach to fabricating nearly arbitrary 2D and 3D geometries at the nanometer-scale. Complex scaffold and staple routing needed to design wireframe DNA origami objects, however, render fully automated, geometry-based sequence design approaches essential for their synthesis. And wireframe DNA origami structural fidelity can be limited by wireframe edges that are composed only of one or two duplexes. Here we introduce a fully automated computational approach that programs 2D wireframe origami assemblies using honeycomb edges composed of six parallel duplexes. These wireframe assemblies show enhanced structural fidelity from electron microscopybased measurement of programmed angles compared with identical geometries programmed using dual-duplex edges. Molecular dynamics provides additional theoretical support for the enhanced structural fidelity observed. Application of our top-down sequence design procedure to a variety of complex objects demonstrates its broad utility for programmable 2D nanoscale materials.

Rapid Prototyping of Wireframe Scaffolded DNA Origami using ATHENA

“…ATHENA has the option to choose the edge type; DNA doublecrossover (DX or 2HB) or six-helix bundle (6HB) that consists of every edge of the 2D or 3D wireframe objects (Figure 1(a); ii). Then, fully automated scaffold and staple sequence design can be performed using either DX- (3,15) or 6HB-edge (16,17) motifs with either the default, M13 ssDNA scaffold, or a custom scaffold of length and sequence defined by the user (Figure 1(a); iii). In addition, the minimum edge length is assigned to the shortest edge, which is then used to scale all other edges, specifying from 42-bp (13.9 nm) to 210-bp (71.1 nm) edge-lengths in the design, which may range from 20 nm to 200 nm for 2D and from 20 nm to 100 nm for 3D when using the M13mp18 ssDNA scaffold (7,249-nt).…”

“…The 6HB edge-based 2D and 3D assemblies showed significantly enhanced mechanical stiffness with respect to DX-edges, highlighting the potential of using wireframe DNA origami for constructing complex nanoscale materials facilitated by automatic design procedures (17).…”

“…Soon after, Douglas et al, applied Rothemund's approach to self-assemble 3D assemblies (7) based on similar design rules, and also released the widely used software tool caDNAno (8) to assist in the manual design of this class of scaffolded DNA origami in which DNA duplexes are arranged on parallel honeycomb or square lattices, also termed "bricklike" origami. While caDNAno has proven extremely useful for the manual scaffold routing and semiautomated sequence design of complementary staples used to self-assemble or fold target shapes, it has limited utility for curved and bent assemblies that require manual insertions and/or deletions in order to induce bend or twist (9,10), or a new class of wireframe scaffolded DNA origami assemblies that render complex 2D and 3D target geometries based on simple wireframe "meshes" (3,(11)(12)(13)(14)(15)(16)(17)(18).…”

Increasing Complexity in Wireframe DNA Nanostructures

“…In addition to PERDIX and TALOS, an algorithm METIS (Mechanically Enhanced and Three-layered origami Structure) [82,83] was developed to enhance mechanical stiffness and fidelity of vertex angles in 2D wireframe origami. This is achieved by combining the above-mentioned methods; now the requirement of full turn (10.5 bp) of double helix at the design edges is not necessary.…”

“…Copyright American Chemical Society, 2019. (f) reproduced with permission from [82]. Published by Springer Nature Ltd., 2019.…”