MgCl2 was 20 mM. The increase in Mg2+ concentration led the nanoscissors to switch from an open to a closed formation (Figure 3.1b). The reverse change was subsequently investigated by decreasing Mg2+ concentration by adding Mg‐free buffer solution to the observation buffer, resulting in the nanoscissors opening again. This example demonstrates the potential of time‐lapse AFM to directly visualize continuous reversible structural changes on the single nanostructure level.
Figure 3.1 DNA origami nanoscissors exhibiting open/closed switching in response to Mg2+ concentration. (a) Schematic drawing of the nanoscissors with shape‐complementary recession‐protrusion patterns. (b) Time‐lapsed AFM images of nanoscissors depicting Mg2+ concentration‐dependent configuration switching. The concentration of MgCl2 was changed while keeping the same area scanned: Left, 5 mM; middle, 20 mM; right, 7 mM. Note that 5 mM of NaCl was also added to the observation buffer to weaken the electrostatic interaction between the nanoscissors and mica surface. The dashed‐circled NSs exhibited reversible switching from open to close and vice versa.
Source: Willner et al. [34]/with permission from John Wiley & Sons, Inc.
Na+‐ or K+‐responsive DNA origami nanodevices are often realized by employing G‐quadruplex formations [29]. The bending molecular actuator that undergoes large deformation in response to K+ was constructed by designing serially repeated tension‐adjustable modules, the cumulative actuation of which resulted in a large deformation of the entire structure, which transformed from a linear shape into an arched shape [36] (Figure 3.2). Each tension‐adjustable module contained single‐stranded bridges containing a human telomeric repeat sequence, which forms a G‐quadruplex in the presence of K+ but dissociates into single strands in the absence of K+. Upon G‐quadruplex formation, the bridge contracted, thereby causing the bending of the module (Figure 3.2a). Through the cumulative effect of this actuation, the entire shape was deformed from the original linear shape into an arched shape (Figure 3.2a). This G‐quadruplex‐formation‐induced actuation was successfully assessed by directly visualizing morphological changes triggered by injecting a high concentration of KCl. Figure 3.2b shows a clear deformation from the relaxed linear shape into the arched shape, which was also reflected in the sudden decrease in the end‐to‐end distances at around 6–8 seconds (Figure 3.2c) and the nearly constant contour lengths of 300 nm that agreed well with the theoretical values for the structure.
Figure 3.2 G‐quadruplex induced large deformation of the DNA origami bending actuator. (a) Schematic drawing of the reversible deformation of the nanoarm carrying the G‐quadruplex forming bridge strands. (b) Time‐lapsed AFM images (0.5 frames/second) of K+‐induced deformation of DNA origami nanoarms carrying G‐quadruplex‐forming sequences. While the scanning area was visualized, 30 μl of 1.0 M KCl in a buffer (5 mM Tris–HCl [pH 8.0], 1 mM EDTA, and 15 mM MgCl2) was injected into 130 μl of the buffer in the observation system, so that the final concentration of KCl was 200 mM. The injection was started at 0 second. Scale bar: 200 nm. (c) Changes in the contour lengths and end‐to‐end distances over a time period.
Source: Suzuki et al. [36]/with permission from John Wiley & Sons, Inc.
3.4 Photoresponsive Devices
A variety of DNA nanodevices capable of performing rotations have been realized by employing strand displacement reaction [19, 31,37–39], B–Z transition [40], and combination of metal ion–DNA complex with i‐motif formation [41]. However, these approaches require dilution of the system or lead to by‐product accumulation, causing decreasing yield rates during continuous manipulation. Incorporation of photochromic molecules into the DNA strands can be employed to avoid steps required to remove undesired reaction by‐products [42–44], and thus provide the possibility of manipulating nanodevices by simple photocontrol [45, 46].
In the design of the rotary device reported by Yang et al., a bar‐shaped DNA rotor was functionalized with photoresponsive DNA motifs and incorporated into the rectangular DNA origami stator [47] (Figure 3.3). A bar‐shaped rotor is composed of two double‐crossover (DX) tiles linked with a rigid shaft synthesized from an oligonucleotide‐oligo (phenylene ethynylene, OPE) [48] (Figure 3.3a,b). The two photoresponsive DNA motifs, OFF‐ and ON‐switching motifs, carry azobenzenes and act as switches to release or lock the rotor at specific orientations on the stator in response to photoirradiation. The OFF‐switching motif is composed of two pseudocomplementary oligonucleotides, OFF‐1 and OFF‐2, carrying four and three azobenzene molecules, respectively, enabling their dissociation under UV and association under visible light (Vis) irradiation (Figure 3.3c). The ON‐switching motif is also composed of two oligonucleotides (ON‐1 and ON‐2); however, each strand carries three azobenzenes and forms a loop and stem segment in an intramolecular fashion, leaving a sticky end (Figure 3.3d). Upon UV irradiation, the stem segment of ON‐switching motifs dissociates to open, followed by hybridization between complementary segments of ON‐1 and ON‐2. The OFF‐1 and ON‐1 motifs were individually introduced into terminals of the rotor (azo‐rotor), while two OFF‐2 and two ON‐2 counterpart motifs were placed at four symmetrical anchoring positions on the origami stator (Figure 3.3e).
Figure 3.3 Photoregulated DNA rotary device. (a) A bar‐shaped rotor composed of two DX tiles joined by a rigid shaft synthesized from an oligonucleotide‐oligo(‐phenylene ethynylene) conjugated component. (b) AFM image of the rotor containing two DX tiles. Scale bar = 50 nm. (c) OFF‐switching motifs (OFF‐1 and OFF‐2): a pair of pseudocomplementary strands containing seven azobenzenes, which dissociated after UV irradiation. (d) ON‐switching motifs (ON‐1 and ON‐2): a pair of hairpin DNA structures containing three azobenzenes in each strand that formed a 10 bp duplex after UV irradiation. (e) Construction of the DNA rotary system and its conversion under photoirradiation. OFF‐1 and ON‐1 strands were incorporated into both terminals of the rotor (azo‐rotor). Two OFF‐2 (anchorages 1 and 2) and two ON‐2 (anchorages 3 and 4) strands were introduced into the DNA origami stator. The azo‐rotor was trapped at anchorages 1 and 2 by the formation of the OFF duplex in the perpendicular state (A or A′). The azo‐rotor was trapped at anchorages 3 and 4 by the formation of the ON duplex in the parallel state (B or B′). The releasing and trapping of the azo‐rotor were regulated by photoirradiation with UV and visible light
