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HS‐AFM is often applied to monitor quick mechanical motions triggered by ions and small molecules. One successful example is visualizing the configuration switching of DNA origami nanoscissors, which has blunt ends on the self‐shape‐complementary recession–protrusion patterns on the surface [34] (Figure 3.1). Since DNA is a negatively charged polymer, there is electrostatic repulsion between DNA helices; however, this repulsion can be weakened by increasing the concentration of divalent cations (such as Mg²⁺), enabling interaction between the shape‐complementary interfaces, which are further stabilized by blunt‐end stacking. Based on this mechanism, the multilayer DNA origami nanoscissors exhibit switching behavior from open to closed and vice versa were developed [35] (Figure 3.1a). For the direct visualization of Mg²⁺ concentration‐dependent changes, the open nanoscissors were first adsorbed onto a mica surface and imaged at an Mg²⁺ concentration of 5 mM. While the scanned area was visualized, buffer containing a high concentration of MgCl₂ was injected into the observation system, so that the final concentration of 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.