It was first suggested 1 more than 30 years ago that Watson-Crick base pairing might be used to rationally design nanoscale structures from nucleic acids. Since then, and especially since introduction of the origami technique 2 , DNA nanotechnology has seen astonishing developments and increasingly more complex structures are being produced [3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18] . But even though general approaches for creating DNA origami polygonal meshes and design software are available 14,16,17,[19][20][21] , constraints arising from DNA geometry and sense/antisense pairing still impose important restrictions and necessitate a fair amount of manual adjustment during the design process. Here we present a general method for folding arbitrary polygonal digital meshes in DNA that readily produces structures that would have been very difficult to realize with previous approaches. This is achieved with a high level of automation of the design process, which uses a routing algorithm based on graph theory and a relaxation simulation to trace scaffold strands through the target structures. Moreover, unlike conventional origami designs built from closed-packed helices, our structures have a more open conformation with one helix per edge and are thus stable in salt conditions commonly used in biological assays.The starting point of the present method is a 3D mesh representing the geometry one wishes to realize at the nanoscale. Focusing only on polyhedral meshes, i.e. meshes which enclose a volume inflatable to a ball, and in contrast to several previous approaches 14,17,19 (see Extended Data Fig. 1) we aim to replace the edges of the mesh by single DNA double helices such that the scaffold strand traverses each of these edges once. This problem is closely related to the Chinese Postman Tour problem 22 in graph theory, which we use to find solutions as doing so by hand would be practically impossible for most meshes. The main principles underpinning our design paradigm are that the technique should allow meshes to be triangulated to optimize structural rigidity; that each edge should be represented by one double helix to enable construction of large structures using as little DNA as possible (though some meshes require two helices to render certain edges as discussed below); and that vertices should be nonBenson et. al, -DNA Rendering of Polyhedral Meshes at the Nanoscale Confidential 2 crossing (i.e. the scaffold should not cross itself in the vertices to ensure non-knotted paths with fewer topological-and kinetic traps during folding, and planar vertex junctions that avoid mesh protrusions due to stacking of crossing helices at each vertex).The overall design scheme is split into four discrete steps: i) Drawing of a 3D polygon mesh in a 3D software, Fig. 1a. ii) Generating an appropriate routing of the long scaffold strand through all the edges of the mesh, Fig. 1b-e. iii) Determining the least strained DNA helix arrangement realizing the 3D mesh, Fig. 1f-i. And iv), Optional fine tuning of the des...

The use of DNAa sananoscale construction material has been ar apidly developing field since the 1980s, in particular since the introduction of scaffolded DNAorigami in 2006. Although software is available for DNAo rigami design, the user is generally limited to architectures where finding the scaffold path through the object is trivial. Herein, we demonstrate the automated conversion of arbitrary twodimensional sheets in the form of digital meshes into scaffolded DNAn anostructures.W ei nvestigate the properties of DNA meshes based on three different internal frameworks in standardf olding buffer and physiological salt buffers.W e then employ the triangulated internal framework and produce four 2D structures with complex outlines and internal features. We demonstrate that this highly automated technique is capable of producing complex DNAn anostructures that fold with high yield to their programmed configurations,c overing around 70 %more surface area than classic origami flat sheets.Since its introduction in the 1980s, [1] DNAn anotechnology has been arapidly growing and diversifying field. This growth has accelerated since the introduction of scaffolded DNA origami in 2006.[2] In aDNA origami structure,along strand, called the scaffold, traverses the entire structure pairing with hundreds of oligonucleotides,c alled staple strands,t hat hold the structure together.The structures are often based around as quare or honeycomb lattice [3] where finding the scaffold path and designing staples is relatively easy,e specially when using software like caDNAno.[4] DNAn anostructures based on small polyhedra have been demonstrated with both scaffolded [5] and non-scaffolded [6] designs.S caffolded DNA nanostructures based on meshwork designs have also been demonstrated with crossing four-arm junctions, [7] with others containing meshes with two DNAd ouble helices per edge. [8] However,n og eneral strategy for producing arbitrary wireframe 2D structures has been demonstrated.Am ajor branch of research has been the addition of functional elements to DNAn anostructures to give them novel properties.C arbon nanotubes and metal nanoparticles have been added for electronic [9] and plasmonic [10] applications.P roteins have been added for templating enzymatic reactions [11] or cell signaling studies. [12] Fluorophores have been added to study energy transfer [13] and to create nanoscale barcodes.[14] DNAo rigami structures have also been used to control the shape of metal particles [15] and graphene sheets.[16] Demonstrations of drug loading [17] and lipid encapsulation [18] indicate that DNAn anostructures could serve as drug delivery tools.M any applications rely on single layer DNAo bjects as they offer the largest 2D canvas for functionalization and are rigid when immobilized on surfaces.Building on Rothemunds method [2] fors caffolded DNA nanostructures,w er ecently developed am ethod for automatically generating wireframe structures from polyhedral meshes. [19] This method relies on an algorithm for finding an E...

DNA origami is a powerful method for the creation of 3D nanoscale objects, and in the past few years, interest in wireframe origami designs has increased due to their potential for biomedical applications. In DNA wireframe designs, the construction material is double-stranded DNA, which has a persistence length of around 50 nm. In this work, we study the effect of various design choices on the stiffness versus final size of nanoscale wireframe rods, given the constraints on origami designs set by the DNA origami scaffold size. An initial theoretical analysis predicts two competing mechanisms limiting rod stiffness, whose balancing results in an optimal edge length. For small edge lengths, the bending of the rod's overall frame geometry is the dominant factor, while the flexibility of individual DNA edges has a greater contribution at larger edge lengths. We evaluate our design choices through simulations and experiments and find that the stiffness of the structures increases with the number of sides in the cross-section polygon and that there are indications of an optimal member edge length. We also ascertain the effect of nicked DNA edges on the stiffness of the wireframe rods and demonstrate that ligation of the staple breakpoint nicks reduces the observed flexibility. Our simulations also indicate that the persistence length of wireframe DNA structures significantly decreases with increasing monovalent salt concentration.

The use of DNA as a nanoscale construction material has been a rapidly developing field since the 1980s, in particular since the introduction of scaffolded DNA origami in 2006. Although software is available for DNA origami design, the user is generally limited to architectures where finding the scaffold path through the object is trivial. Herein, we demonstrate the automated conversion of arbitrary two‐dimensional sheets in the form of digital meshes into scaffolded DNA nanostructures. We investigate the properties of DNA meshes based on three different internal frameworks in standard folding buffer and physiological salt buffers. We then employ the triangulated internal framework and produce four 2D structures with complex outlines and internal features. We demonstrate that this highly automated technique is capable of producing complex DNA nanostructures that fold with high yield to their programmed configurations, covering around 70 % more surface area than classic origami flat sheets.

We address the problem of de novo design and synthesis of nucleic acid nanostructures, a challenge that has been considered in the area of DNA nanotechnology since the 1980s and more recently in the area of RNA nanotechnology. Towards this goal, we introduce a general algorithmic design process and software pipeline for rendering 3D wireframe polyhedral nanostructures in single-stranded RNA. To initiate the pipeline, the user creates a model of the desired polyhedron using standard 3D graphic design software. As its output, the pipeline produces an RNA nucleotide sequence whose corresponding RNA primary structure can be transcribed from a DNA template and folded in the laboratory. As case examples, we design and characterize experimentally three 3D RNA nanostructures: a tetrahedron, a bipyramid and a prism. The design software is openly available, and also provides an export of the targeted 3D structure into the oxRNA molecular dynamics simulator for easy simulation and visualization.