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The formation and disruption of a single G‐quadruplex structure were observed in nanospace [59]. To observe G‐quadruplex formation, two dsDNA strands containing single‐strand G‐rich overhangs in the middle of an interstrand G‐quadruplex were attached to a DNA frame (Figure 1.9a). Three G‐tracts were placed in the upper G‐strand, whereas the lower strand had a single G‐tract [63]. In the presence of K⁺, the formation of an interstrand G‐quadruplex was observed in 44% yield (X‐shape). The dynamic formation of the G‐quadruplex was directly observed in real time using HS‐AFM. During scanning of the sample in the presence of K⁺, the two G‐strands maintained a separated state for a given period, then spontaneously formed the G‐quadruplex which was observed as an X‐shape. In a similar fashion, we observed the disruption of G‐quadruplexes in the absence of K⁺. The X‐shape was unchanged for a period of time, then separated under AFM scanning.

In addition, we directly visualized the rotary motion of a B–Z conformational transition in the DNA frame [60]. To visualize the B–Z transition, dsDNA containing a 5‐methyl‐CG (^5meCG) six‐repeat sequence (B–Z system; upper strand) and a flag marker containing three‐helix‐bundled DNA connected by crossovers was introduced to the DNA frame (Figure 1.9b). During the B–Z transition, the flag marker rotates around the dsDNA shaft, and the rotary motion can be observed by monitoring the position of the marker. By controlling the concentration of Mg²⁺ ions under equilibrium conditions for the B–Z transition, the movement of the flag marker in the B–Z system was observed during HS‐AFM scanning. The change in height of the flag marker could also be observed, further indicating that rotation around the dsDNA shaft occurred in the B–Z transition system.