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 origami with five cavities, we introduced substrate DNA strands with recognition sequences into each cavity [45]. The Zn‐finger proteins directly bound to the cavity containing the target sequence with 50–80% yield. In addition, GFP‐fused Zn‐finger proteins retained sequence‐specific recognition ability, albeit with a lower binding affinity. These results show that proteins can be directly targeted to specific sites using sequence‐selective Zn‐finger proteins. In addition, a sequence‐specific DNA recognition molecule, pyrrole‐imidazole polyamide was able to recognize and bind to the target sequences on DNA origami [46, 47]. We used a DNA origami structure with five cavities, into which five different sequences were incorporated. We visualized the selective alkylation of a biotinylated polyamide to the target sequence with streptavidin labeling. Using this method, the polyamide was found to alkylate the target sequence in 88% yield by discriminating one‐base mismatches. Selective alkylation and subsequent streptavidin labeling revealed the sequence selectivity of the polyamide at the single‐molecule level.
1.5.3 Distance‐Controlled Enzyme Reactions and Photoreactions
Yan and coworkers created a distance‐dependent enzymatic cascade on a DNA origami surface. Individual pairs of glucose oxidase (GOx) and HRP were placed at specific positions on the DNA origami with controlled spacing (Figure 1.6c) [37]. The distances between the enzymes were systematically changed from 10 to 65 nm, and their activities were evaluated. Two different distance‐dependent kinetics were observed between the assembled enzyme pairs, and by incorporating the intermediate protein, the activity was enhanced due to the hydration shells.
Stein and coworkers performed a combination of multistep energy transfer in a photonic wire‐like structure using an energy‐transfer cascade [38]. Fluorophores that allow alternative energy‐transfer pathways to proceed, depending on the incorporation of a jumper dye, were arranged on a DNA origami surface (Figure 1.6d). An input dye (ATTO488), two output dyes (red fluorophore ATTO647N and IR fluorophore Alexa 750), and two jumper dyes (ATTO565) were placed onto three helices to minimize fluorophore interactions throughout the DNA molecule. Single‐molecule four‐color FRET by laser excitation was used in this study. As designed, the energy‐transfer pathways from blue to red or blue to IR dyes were successfully controlled at the single‐molecule level by the presence of the jumper dyes, which directed the excited‐state energy from the input dye to the output dyes. These results indicate that DNA origami might serve as a circuit board for photonic devices beyond the diffraction limit and at the molecular scale.
These studies show that molecules and nanoparticles can be selectively incorporated into DNA origami, and the enzymatic cascade reactions and energy transfer pathways were controlled in a distance‐ and position‐dependent manner. These systems are relatively easily constructed by the placement of proteins via a corresponding ligand and hybridization of DNA with functional molecules and nanoparticles onto the addressable DNA origami nanostructures.
1.6 Single‐Molecule Detection and Sensing using DNA Origami Structures
1.6.1