DNA Origami. Группа авторов
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DNA strands. AuNPs of different sizes were placed on the PX‐JX2 devices and were transferred to the DNA walker by rotating motion at specific positions. These results show that the DNA walker moved on the track unidirectionally that the delivery of AuNPs was controlled by the PX‐JX2 devices, and that they were transferred to the DNA walker. After the completion of this process, DNA walkers with three different AuNPs bound were obtained with a yield of 43%. As the PX‐JX2 device can control the ON–OFF switching of the transfer of AuNPs using specific DNA strands, the product was obtained in high yield (>90%), and the error rate was suppressed (1%). In addition, eight patterns of capture of AuNPs onto the DNA walker were achieved using three PX‐JX2 devices with the ON–OFF switching operation of these devices.
1.9.2 DNA Spider System Constructed on the DNA Origami
Stojanovic and coworkers created DNA nanomachines called “DNA spiders” on various path patterns constructed on DNA origami (Figure 1.11b) [87]. The DNA spiders consisted of three DNA strand legs and one capture DNA strand (capture leg). The three legs of the DNA spiders each contained a DNA enzyme (DNAzyme leg) that could hydrolyze RNA. Single‐stranded DNAs containing a cleavable RNA site were arranged on DNA origami as a track for the DNA spider to walk. The DNA spider was immobilized at a specific position on the DNA origami using a trapping DNA strand, followed by dissociation and initiation of walking on the track. The DNA spider bound to the ssDNAs on DNA origami, cleaved the RNA site in the ssDNAs using its DNAzyme function, and walked autonomously. The DNA spider moved forward along the predetermined track and finally stopped at a specific point on the DNA origami where ssDNAs did not have an RNA site for cleavage. All of these processes, including initiation, walking, and stopping, were controlled in a programmed manner. In addition, by measuring the position of the DNA spider on DNA origami using super‐resolution microscopy, it was found that the spider moved at a speed of 3 nm/min.
Figure 1.11 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.
Source: Gu et al. [86]/with permission of Springer Nature.
The DNA walker stops at three places on DNA origami and receives AuNPs (C1–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 contains RNA) in the track. DNAzyme for cleavage of RNA site in the ssDNA is introduced to three legs.
Source: Lund et al. [87]/with permission of Springer Nature.
DNA strands in the track before and after cutting (gray and light gray circles) and stopping DNA strands (right side 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). (c) A DNA motor system created on the DNA origami. A motor‐track (gray ssDNAs) was constructed on the DNA origami and the movement of the DNA motor (black ssDNA) was examined.
Source: Wickham et al. [88]/with permission of Springer Nature.
Stepwise movement of a DNA motor observed in real time by high‐speed AFM.
1.9.3 DNA Motor System Constructed on the DNA Origami
We created a DNA transportation system in which a DNA nanomachine can move along a designed track constructed on DNA origami (Figure 1.11c) [88]. A track consisting of multiple ssDNAs (17 stators) was constructed on a DNA scaffold for observation of the multistep movement of a specific DNA motor strand. When a motor strand hybridizes to the complementary stator, cleavage by a nicking enzyme induces branch migration to move one step forward (Figure 1.11c) [89]. Multistep movement was achieved by the turnover of the enzymatic reactions. AFM imaging of the motor strand indicated a single spot of the duplex on the DNA origami, and one‐directional and time‐dependent movement of the DNA motor strand was observed along the motor track. Furthermore, the movement of the motor strand along the motor track was directly observed by HS‐AFM. The DNA motor moved forward along the motor track in each AFM image, and the distance of the movement of the DNA motor corresponded to the distance between adjacent stators, indicating that the movement occurred stepwise on the track. Furthermore, a complicated system for controlling the direction of the motor movement was designed and constructed using a branched track and controllable blocking strands [90]. The movement of the motor was tracked and induced to one of the final destinations using the programmed instruction.
These complicated mobile systems can only be achieved on a planar DNA origami structure, which can provide a programmed scaffold for construction of the track with predesigned instructions. These are excellent examples of nanoscale molecular systems using the addressability of DNA origami.
1.10 Selective Incorporation of Nanomaterials and the Applications
Position‐controlled placement of nanomaterials has been carried out by employing the addressable property of DNA origami. By directly coupling AuNPs with a staple DNA strand, AuNPs have been selectively placed on DNA origami [34, 35]. Alternatively, thiol groups were first placed on DNA origami structures to assemble AuNPs at predesigned positions [91, 92]. The yield of AuNPs binding improved using the small cavities of the DNA origami structures to accommodate them. Incorporating single‐stranded DNAs on DNA origami controlled the positioning of two DNA‐modified carbon nanotubes into cross‐junctions on both sides of the DNA origami [93]. Position‐controlled carbon nanotubes were applied to create a single‐molecule device, which showed field‐effect transistor‐like behavior.
1.10.1 DNA Origami Plasmonic Structure with Chirality
One applications of DNA origami structures is the development of plasmonic structures that control plasmonic interactions by arranging AuNPs in precise positions. Since DNA origami can create a structure with a size of 10–100 nm, DNA origami used as a template enables precise placement by controlling the distance and orientation of AuNPs and examination of its physical properties. Attachment of AuNPs to DNA origami was carried out by selective hybridization of a DNA‐AuNP conjugate to complementary strands arranged on the DNA origami structure. Liedl and coworkers constructed plasmonic structures with chirality, in which AuNPs were placed precisely on DNA origami [94]. A cylindrical DNA origami structure 100 nm in length was prepared to arrange the AuNPs in right‐handed and left‐handed helices (Figure 1.12a). A DNA strand was bound to the AuNP (10 nm), and a complementary DNA strand was bound to the DNA origami structure. The AuNPs were precisely placed in nine locations on the right‐handed and left‐handed DNA origami. In these plasmonic structures, a circular dichroism (CD) response was observed in the plasmonic absorption region of the AuNPs due to plasmonic interaction between AuNPs and their chirality. Positive and negative Cotton effect signals were observed in the right‐handed and left‐handed helices, in which inverting spectra were observed (Figure 1.12b,c). In addition, when AuNPs with a larger diameter (16 nm) were introduced, the CD signal intensity increased 400‐fold due to the increased interactions. Using DNA origami as a scaffold, the 3D spatial arrangement of AuNPs was accurately designed and the CD spectra were simulated, which was in good agreement with the experimental results. Therefore, this study shows that plasmonic