DNA Origami Nanomachines

Abstract

DNA can assemble various molecules and nanomaterials in a programmed fashion and is a powerful tool in the nanotechnology and biology research fields. DNA also allows the construction of desired nanoscale structures via the design of DNA sequences. Structural nanotechnology, especially DNA origami, is widely used to design and create functionalized nanostructures and devices. In addition, DNA molecular machines have been created and are operated by specific DNA strands and external stimuli to perform linear, rotational, and reciprocating movements. Furthermore, complicated molecular systems have been created on DNA nanostructures by arranging multiple molecules and molecular machines precisely to mimic biological systems. Currently, DNA nanomachines, such as molecular motors, are operated on DNA nanostructures. Dynamic DNA nanostructures that have a mechanically controllable system have also been developed. In this review, we describe recent research on new DNA nanomachines and nanosystems that were built on designed DNA nanostructures.

Keywords: DNA nanomachine; DNA nanotechnology; DNA origami; high-speed AFM; single-molecule analysis.

Figure 1

Operation of DNA machines and creation of nanostructures by DNA origami method. (a) DNA strand displacement reaction via toehold sequence used for operation of DNA nanomachine. (b) DNA tweezers using strand displacement reaction [5]. Set strand controls open to close state of the green DNA strand and unset strand removes the set strand to make open state. (c) The preparation of nanometer scale structure using DNA origami method. Long ssDNA (M13mp18) and short complementary DNA strands (staple DNA) are self-assembled by annealing [1]. When the target molecules (green circle) are bound to the staple DNA, the molecules can be placed at the predesigned positions on the DNA origami structure.

Figure 2

Assembly line with a DNA walker capturing gold particles and DNA spider molecule walking in a track on a DNA origami. (a) The DNA walker binds to the DNA strand on the DNA origami with three legs, and gold particles (AuNPs) are collected with three hands [18]. The DNA walker stops at three places on DNA origami and receives AuNPs (C1, C2, C3) to be transferred by rotating PX-JX₂ DNA devices. Multiple operation on DNA origami and corresponding AFM image. (b) The DNA spider binds onto the DNA origami using three legs hybridized to ssDNAs (cleavage site is RNA) in the track. DNAzyme for cleavage of RNA site in the ssDNA is introduced to three legs [19]. DNA strands in the track before and after cutting (brown and light brown circles) and stopping DNA strands (red circles). The path for walking with instruction (start, follow, turn, and stop) can be programmed on the DNA origami. AFM image of DNA spider molecule walking on the DNA origami track. Start (top), walking (middle), and stop (bottom).

Figure 3

A DNA motor system constructed in the DNA origami structure [20]. (a) A track consisting of 17 ssNAs (green) constructed on a DNA origami structure. The DNA motor strand (red) moves on the track in one direction using enzymatic reaction. (b) Mechanism of DNA motor system using branch migration. After cleavage of nicking enzyme, the DNA motor hybridized to the ssDNA (green) in the track moves to the adjacent DNA strand with the same sequence via intermediate state (branch migration). (c) Single-molecule visualization of the DNA motor using high-speed AFM and its analysis. The DNA motor moved stepwise along the ssDNAs in the track, and the intermediate state of the branch migration could also be visualized. (d) A DNA motor system using a branched track and controllable gates [21]. A track consisting of ssDNAs having three branch points (junctions) and four end points constructed on the DNA origami structure. The DNA motor moves along the ssDNAs in the branched track from the start position. (e) The control of opening the gates constructed on both sides of the branch point by strand displacement. (f) The branched track controlled by multiple gates and the programmed movement of the DNA motor by following the instructions. AFM images of the DNA motor movement directed by the designed instruction.

Figure 4

Reconfigurable DNA origami structures that change their conformation in response to physical stimuli and DNA strands. (a) DNA dynamic nanodevice that responses to temperature and salt concentration. Two domains can rotate around the center axis. The nanodevice reversibly opens and closes in response to temperature [24]. (b) A molecular robot that opens and closes the arms in response to salt concentration. (c) HS-AFM images of conformational changes of the DNA nanodevice with photoswitching strands and UV and Vis irradiation [25]. (d) Reconfigurable DNA nanostructure in left-handed and right-handed locked states controlled by strand displacement with toehold-containing DNA strands [26]. (e) Plasmonic nanostructure with two gold nanorods (AuNR), and locked and relaxed state can be controlled with photo-responsive DNA strands and UV/Vis irradiation [27]. In response to light, a locked state and a relaxed state occur, and spectroscopically read out according to the plasmon interaction between the AuNRs. (f) Reconfigurable DNA origami tripod with AuNRs. Releasing strands (R) and locking strands (L) are employed to stepwise manipulation of the angle between the DNA arms [28].

Figure 5

DNA-based rotary apparatus [32]. (a) Design of assembled rotor apparatus with closed brackets (red) and a locked rotor (blue) (left). Assembled rotary motor apparatus with a mobile rotor (right). (b) Rotary apparatus with a 550 nm crank lever for observation of rotary movement. TEM image of the construct. (c) Observation of rotary movement of single apparatus acquired by TIRF microscopy (left) and sum over all 1500 images (right).

Figure 6

(a) DNA origami channel [33]. Tubular pores (red), main body (gray), cholesterol moieties (orange) at the bottom of the main body and TEM image. (b) The DNA channel is bound to the lipid bilayer membrane via cholesterol, and the pore domain penetrates the lipid bilayer membrane. TEM image of origami channels bound to a liposome. (c) Measurement of nucleosome-nucleosome interaction using reconfigurable tweezer-shaped DNA origami and TEM image [34].

Figure 7

DNA nanorobots with open/close switch for biological applications. (a) Controlled opening of the box lid using toehold containing DNA strands (keys) [37]. (b) DNA nanorobot that recognizes cells and activating signaling pathway in the cell [39]. Nanorobot in a closed state. Antibodies are attached inside the barrel-shaped structure and are closed by DNA strands that used as “locks” (dashed rectangle). (c) Mechanism of opening the structure by use of “key”. The target molecule (red circle) binds to the blue DNA strand (aptamer DNA), and the initial dsDNA dissociates. (d) Nanorobot in an opened state. Internal antibodies bind to cell-specific antigens. The nanorobot opens with two kinds of target molecules, so that only when two molecules exist, it binds to the cell surface. Cells can be Identified in a logic gated way. (e) DNA nanorobot targeting specific tumor [29]. Thrombin is attached to the sheet, and the structure is closed in a tubular shape by aptamers. When a tumor associated target protein is attached to the aptamers, the tubular nanorobot opens to expose the thrombin, which performs blood coagulation at the tumor site.