1 DNA Origami Technology: Achievements in the Initial 10 Years

       Masayuki Endo1,2

       1 Institute for Integrated Cell-Material Science, Kyoto University, Kyoto, Japan

       2 Organization for Research and Development of Innovative Science and Technology, Kansai University, Osaka, Japan

1.1 Introduction

      DNA nanotechnology has grown as a field of research in the past three decades. The technology uses the self‐assembly of DNA molecules that have sequence selectivity, programmability, and periodical double‐helical structure. Self‐assembly is commonly seen in living systems and plays a central role in the formation of cellular structures and thus influences the functions of organized biological systems in the cell. From the viewpoint of molecular science, the precise formation of structures via self‐assembly attracts attention because specific functions can stem from the precise arrangement of the molecules. DNA nanotechnology allows the construction of various self‐assembled scaffolds that are versatile for the placement and arrangement of functional molecules and nanomaterials and for the production of complex molecular devices.

The field of DNA nanotechnology was pioneered by Ned Seeman, who first proposed the concept of DNA nanotechnology in 1982, and then created various DNA motifs and strategies for self‐assembly that constitute the basic concept of structural DNA nanotechnology (Figure 1.1) [1, 2]. DNA nanotechnology now is now applied in the construction of nanoscale structures and functionalized materials and is further used in molecular computation and mechanics and in the fields of chemistry and synthetic biology, and continues to progress in response to technology demands [3–5]. DNA origami, a new form of programmed DNA assembly based on well‐established DNA nanotechnology, enables the design of two‐dimensional (2D) nanostructures with a wide variety of shapes in a defined size [6]. Moreover, functional molecules, enzymes, and nanomaterials have been precisely placed on DNA origami structures, which enables the creation of novel molecular systems, nanoscale devices, and advanced materials [3–5].

      This chapter describes the general introduction of DNA origami and highlights the basics of DNA origami technology, including the design and construction of 2D and three‐dimensional (3D) structures and selective functionalization. In addition, this chapter focuses on its applications in various research fields, including single‐molecule detection and sensing, single‐molecule imaging of biomolecules, molecular machines, plasmonics, dynamic devices, and molecular delivery systems.

Figure 1.1 History of DNA nanotechnology and DNA origami technology. Progress of DNA nanotechnology and DNA origami technology and major findings and inventions in this field.

      1.1.1 DNA Nanotechnology Before the Emergence of DNA Origami

For construction of a large‐sized DNA nanostructure by self‐assembly, rigid DNA building blocks are required. The first DNA building block, the double‐crossover (DX) motif, is one of the most essential and important inventions in DNA nanotechnology [7]. In the DX motif, two double‐stranded DNAs (dsDNA) are connected at two crossover points in parallel and antiparallel arrangements, which reduces the flexibility of the single dsDNA (Figure 1.2c). The two crossover points are separated by a defined number of base pairs. Using these DX tiles as building blocks, large nanostructures can be constructed via hybridization of the four sticky ends introduced to the DX tiles, which directs the self‐assembly into 2D nanostructures [10]. By using this strategy, 2D building blocks have been further developed for the preparation of various 2D tiles, such as triple‐crossover [11], triangular [12, 13], and 4 × 4 tiles [14]. This concept has also been extended to double‐helix bundled building blocks designed for the construction of tubular structures [15]. All the structures were constructed by simply using defined numbers of unmodified DNA strands. For further extension of the nanostructures, a more complicated design of the building blocks and sequences with larger numbers of DNA strands are needed.

      In addition, mechanical DNA nanomachines with a controllable molecular system were developed. An extra sequence called a “toehold” is attached to the end of the DNA strand. Using this toehold, the DNA molecular machines are operated by adding and removing specific DNA strands for complex movements. When a DNA strand fully complementary to a toehold‐containing DNA is added, the initial complementary strand without the toehold is selectively removed by strand displacement [16]. The thermodynamic stabilization energy for hybridization works as “fuel” to provide the mechanical motion of the DNA molecular machine. Using this strategy, DNA tweezers that perform open–close motions were constructed (Figure 1.2d) [8]. Seeman and coworkers created a molecular machine combining DNA nanostructures. Using the helical rotation of dsDNA during the B–Z transition, in which the dsDNA conformation changes from a right‐handed (B‐form DNA) to a left‐handed (Z‐form DNA) conformation, a reciprocating motion of the DNA nanostructure was observed [17]. In addition, they developed molecular machines that perform 180° rotation at the ends of two adjacent dsDNAs, called PX‐JX₂ devices, by hybridization and removal of DNA strands (Figure 1.2e) [9]. Both the PX and JX₂ states were directly observed by atomic force microscopy (AFM). These dynamic systems were also introduced to DNA origami to operate DNA nanodevices (see