caDNAno software, which is publicly available, has been developed to support the design of these 3D structures [28].
Furthermore, using the layered structures described above, new 3D structures were built by changing the helical twist from the average helical pitch of 10.5 bp/turn to either 10 or 11 bp/turn [29]. When dsDNAs with different helical pitches were bundled together, torque and repulsion between base pairs caused overall structural changes including twisting or 30–180° bending. Using these structures as building blocks, left‐handed or right‐handed helical ribbon structures were prepared. In addition, when angle‐controlled duplex bundles were connected to each other, a six‐tooth gear and a spherical wireframe capsule were created.
Figure 1.5 Design and construction of three‐dimensional DNA origami structures. (a) Scheme for folding the 2D pleated structure into a 3D multilayered structure using staple strands connecting adjacent layers. Sectional views of the positions of the crossovers in the multilayered structure sliced at seven‐base‐pair intervals. (b) Global twisted structures of six‐helix DNA bundles obtained by the selective deletion or insertion of nucleotides to change the helical turns from the normal 10.5 base pairs to 10 or 11 base pairs. TEM images of the polymerized ribbons containing 10.5‐, 10‐, and 11‐base‐pair helical pitches.
Source: Douglas et al. [25]/with permission of Springer Nature.
(c) DNA box structure by folding of six DNA origami rectangles using interconnection strands introduced at the edges of rectangles. The DNA box model reconstructed from cryo‐EM images.
Source: Andersen et al. [26]/with permission of Springer Nature.
(d) Spherical shells, ellipsoidal shells, and nanoflask DNA origami using combination of curved dsDNAs.
Source: Han et al. [27]/with permission of American Association for the Advancement of Science.
Using a different strategy, a DNA box structure was created by folding multiple 2D origami domains with interconnecting strands [26]. Six independent rectangles were sequentially linked and were designed to be folded using interconnection strands in a programmed fashion (Figure 1.5c). Analyses of the assembled structure by AFM, cryo‐electron microscopy, dynamic light scattering, and small‐angle X‐ray scattering indicated that the size was close to the original design. The lid of the box could be opened using a specific DNA strand to release the closing duplex by strand displacement, and the opening event was monitored by fluorescence resonance energy transfer (FRET). Other types of DNA boxes have been created using a similar method, which can control both the inside and outside by adjusting the directions of the crossovers at the connection edges [30, 31]. A tetrahedral structure was designed and constructed from four aligned origami triangles, which were preconnected with an M13 scaffold strand without folding independent 2D plates [32]. Using the strategy of folding 2D origami structures, we designed and prepared new hollow triangular, square, and hexagonal prism structures [33]. The opening event of these prism structures was observed in real‐time and characterized using high‐speed AFM.
Yan and coworkers [27] created more complex rounded 3D structures, such as spheres by using a combination of curved dsDNAs (Figure 1.5d). By designing and arranging the nanorings, positions of crossovers and helical pitches for preparing the curvatures of the nanoring structures were examined. For the preparation of planar curvature, concentric rings of DNA were prepared by rationally designed geometries and crossover networks. In addition, nonplanar curvatures were created by adjusting the position and pattern of crossovers between adjacent dsDNAs to change the helical pitches from the native B‐form twist. Finally, round‐shaped 3D nanostructures such as spherical shells, ellipsoidal shells, and a nanoflask were created.
1.5 Modification and Functionalization of 2D DNA Origami Structures
1.5.1 Selective Placement of Functional Nanomaterials
One of the most important features of DNA origami is that each individual position in the origami structure contains different sequence information. This means that functional molecules and particles attached to the staple strands can be specifically placed at desired positions on the origami structure. DNA origami is a versatile scaffold for the functionalization of relatively large molecules and nanoparticles. The surface of the DNA origami has different sequences at all positions, meaning that the individual sequences correspond to individual addresses in the origami structure. Using a rectangular DNA origami tile, gold nanoparticles (AuNPs) and proteins were attached at specific target positions on the surface. Single and double AuNPs were directly incorporated at specific positions on DNA origami using synthetic DNA‐AuNP conjugates [34]. DNA‐AuNP conjugates connected by double thiol groups attached to the DNA tile in 91% yield. Furthermore, three different sizes of AuNPs (5, 10, and 15 nm) were site‐selectively incorporated into triangular DNA origami in around 50% yield (Figure 1.6a) [35]. The multiple metal nanoparticle complexes can be assembled programmably and can be stably purified by gel electrophoresis.
Figure 1.6 Selective incorporation of nanoparticles, proteins, enzymes, and functional molecules onto the DNA origami structures. (a) Selective placement of different size of AuNPs on DNA origami.
Source: Ding et al. [35]/with permission of American Chemical Society.
(b) Stepwise and selective placement of proteins using a ligand and counterpart tag protein binding.
Source: Sacca et al. [36]/with permission of John Wiley & Sons, Inc.
(c) Two‐enzyme‐coupled cascade [glucose oxidase (GOx) and horseradish peroxidase (HRP)] constructed on the DNA origami.
Source: Fu et al. [37]/with permission of American Chemical Society.
(d) Arrangement of fluorophores on DNA origami to control the direction of energy transfer. FRET‐related ratios from blue to red (E*br) and from blue to IR (E*bir) for the four different origami samples. Dark gray, light gray, and black spheres represent the input, jumper and output dyes, respectively. White sphere indicates the absence of jumper dye.
Source: Stein et al. [38]/with permission of American Chemical Society.
1.5.2 Selective Placement of Functional Molecules and Proteins via Ligands
Proteins have been selectively attached to the DNA origami structures by conjugating ligands and aptamers to staple strands [39–42]. The combination of specific proteins and ligands, such as SNAP‐tag and Halo‐tag, was also used for the selective placement of fusion proteins on DNA origami (Figure 1.6b) [36]. Zn‐finger proteins are sequence‐selective DNA‐binding molecules, and the specific binding sequence can be determined by designing the amino acid sequences [43, 44]. Using DNA
