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].
Using the techniques developed in these studies, functional molecules and nanoparticles can be selectively placed at specific positions of DNA origami in a programmed fashion. In addition, DNA origami can be integrated with top‐down nanotechnology. These methods could be applied for creating nanoscale devices with novel functionality when the functional origami is precisely integrated on the fabricated surface.
1.11 Dynamic DNA Origami Structures Responsive to External Stimuli
1.11.1 DNA Origami Structures Responsive to External Stimuli
DNA origami technology enables the creation of robust 3D structures, which can perform various mechanical movements [98, 99]. A dynamic DNA origami that changes 3D structure in response to external stimuli such as salt concentration and temperature was developed. In the design, shape fitting and π–π stacking interactions between the base pairs were utilized. As shown in (Figure 1.13a), the DNA origami consists of two shape‐complementary rods that can rotate around the pivot, and the opened X‐shaped structure closes into a closed rod shape depending on the salt concentration [100]. By detecting open and close states by fluorescence, the structure operated more than 1000 open/close cycles without breaking by heating and cooling. The performance and robustness as a mechanical molecular device were excellent. Furthermore, a movable grid assembly at the micrometer scale was constructed by further assembling the dynamic DNA origami. In combination with these mobile parts, as a demonstration, a nanoscale “human‐shaped robot” was also constructed, that can open and close the arms by controlling the salt concentration (Figure 1.13b). Using DNA origami in this way, it is possible to create designable self‐assembled materials that can be driven in response to various external stimuli.
1.11.2 Stimuli‐Responsive DNA Origami Plasmonic Structures
A DNA origami nanodevice that controls the plasmonic interaction between two gold nanorods (AuNRs) was constructed by controlling the rotation of the structure. A structure with two plates (80 nm × 16 nm × 8 nm) was created that could rotate at the central connection (Figure 1.13c) [102]. The direction of rotation could be controlled by selective DNA strand displacement. The conformations of the structures were characterized by CD due to the chirality generated from DNA and the plasmonic interaction between the two AuNRs. Depending on the sequence of the toehold‐containing DNA strands, the structure can form a relaxed or locked state and rotate to the right or left in a programmed fashion. Stepwise reactions can be directly monitored by detecting changes in the CD spectra.
1.11.3 Photo‐Controlled DNA Origami Plasmonic Structures
Photoswitches were incorporated into the DNA origami plates to control the locked and relaxed states of the AuNR‐bound plates by photoreaction (Figure 1.13d) [101]. Photoresponsive DNA strands containing a photoisomerizable azobenzene derivative were incorporated into the sides of the two plates. Dissociation and binding of the photo‐responsive DNA strands by UV and visible light irradiation induced the open (relaxed state) and closed (locked) states, respectively. Two AuNRs (40 nm × 10 nm) were attached to each plate via hybridization of DNA strands introduced to the AuNRs and the plates. CD bands were observed at around 740 nm in the spectrum when the two plates were locked by hybridization of photoresponsive DNA strands. When the two plates were relaxed by dissociation of the photoresponsive DNA strand, the CD signals cancelled out and became extremely weak because the angle between the two arms was not fixed. Because of the reversibility of the cis–trans photoisomerization of azobenzene, two conformations (relaxed and locked state) could be repeatedly formed by alternating UV and visible irradiation, and conformational changes could be read spectroscopically in real time. The results show that these dynamic DNA origami devices can be used for molecular memory by reading out the reversible conformational change induced by photoirradiation.