DNA Origami. Группа авторов

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      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 materials with predicted physical properties can be designed and constructed.

Figure 1.12 Helical AuNP plasmonic structures constructed on a DNA origami. (a) Left‐handed (LH) and right‐handed (RH) helical structures (diameter 34 nm, helical pitch 57 nm) with 9 AuNPs (10 nm) bound to the surface of a 16 nm diameter DNA origami. (b) Left‐handed (LH) and right‐handed (RH) CD spectra (left) of the helical structure of AuNPs (10 nm) and its simulated spectra (right). (c) Left‐handed (LH) and right‐handed (RH) CD spectra of a spiral structure of AuNPs (16 nm) (left) and their simulated spectra (right). (d) Surface‐enhanced fluorescence from two AuNPs‐bound DNA origami tower structure standing on a glass surface. Using a tower structure with two AuNPs (80 nm), the DNA strand to which the dye was bound transiently emits light that repeatedly binds and dissociates to the complementary strand DNA placed in the gap between the AuNPs.

      Source: Kuzyk et al. [94]/with permission of Springer Nature.

      1.10.2 Surface‐Enhanced Fluorescence by Gold Nanoparticles and DNA Origami Structure

      Surface‐enhanced fluorescence using AuNPs can be applied in various fields such as highly sensitive single‐molecule detection, biomolecule sensing, and nanoscale optical control. This surface enhancement effect depends on the size and shape of the AuNP and the relative position with respect to the fluorescent molecule. Therefore, the technical question is whether the excited plasmons of the AuNPs can be coupled and the fluorescent molecules can be fixed to the electric field “hot spot” that is locally enhanced. Studies have been conducted to systematically control surface‐enhanced fluorescence by designing the size and position of multiple AuNPs and the position of fluorescent molecules using a DNA origami structure [95]. Two AuNPs (100 nm) were fixed to a tower‐shaped DNA origami structure (height 220 nm, diameter 15 nm) with a gap of 23 nm, and dye molecules were introduced into the space (Figure 1.12d). By using this structure, the fluorescence of the dye molecules located in the hot spots between AuNPs was enhanced up to 117 times. Using this plasmonic structure, a single‐stranded DNA strand (anchor) was placed at the hot spot, and single‐molecule binding and dissociation of a complementary strand DNA strand to a dye molecule was detected (Figure 1.12d). Dynamic single‐molecule detection of biomolecules in a short time (~10 μs) at low excitation energy was realized with this system.

      1.10.3 Placement of DNA Origami onto a Fabricated Solid Surface

      DNA origami can be fitted and made compatible with solid materials made by semiconductor processing. Triangular origami binding sites on a surface were fabricated by electron beam lithography and dry etching. For the alignment of triangular origami, their binding sites were fabricated on a SiO₂ surface passivated with trimethylsilane (TMS) or origami binding sites on diamond‐like carbon (DLC). Using this method, triangular origami was selectively fitted to the binding sites depending on the size of the binding sites [96]. The hydrophilicity of the surface of the binding sites passivated with TMS is considered to be a driving force for binding. Using various shapes of binding sites on the surface, multiple origami triangles were selectively attached. Using a similar method, gold particles bound to the three vertices of a DNA triangle were successfully aligned to the origami binding sites with controlled orientation and arrangement [96, 97].

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