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Mao and coworkers developed a strategy for the detection of a single biomolecule using a DNA origami nanostructure as a mechanochemical platform [51]. A connected seven‐tile DNA origami was designed and six sensing probes were incorporated at different locations on the tiles (Figure 1.8c). Platelet‐derived growth factor (PDGF) was used as a target molecule, and binding of the target to the aptamer induces dehybridization of the complementary strand, opens the lock, and finally induces an expansion of approximately 15 nm (Figure 1.8d). Binding of a target molecule to these probes induces rearrangement of the origami nanostructure, which is monitored in real time using optical tweezers. Without PDGF, no recognition events were observed. This platform can detect 10 pM PDGF within 10 minutes, while the PDGF and a DNA target were differentiated and identified in a multiplexing fashion. The results show that this mechanochemical platform could offer a solution for high‐throughput sensing at the single molecular level.

Figure 1.7 Detection of target RNA by hybridization with probe DNA strands introduced on the DNA origami. (a) Method for imaging the hybridization of target RNA to a probe DNA on the DNA origami. (b) Multiple DNA probes complementary to the target RNAs were introduced onto the DNA origami, and hairpin DNAs were also introduced as an index for identifying the probe strand. (c) AFM images of binding of target RNA to the probe strands. Specific DNA probes can be identified by the corresponding index.

Source: Ke et al. [48]/with permission of American Association for the Advancement of Science.

(d) Single chemical reaction on DNA origami. Reactive groups (azido, amino, and alkyne groups) were incorporated into the DNA origami by conjugation with staple DNA strands. The coupling reactions were then performed using the biotin‐attached functional groups. The completion of the reactions was visualized by the binding of streptavidin. (e) AFM images of the three individual reactions and three successive reactions by the treatment of three biotin‐attached functional groups. Yields are presented below the AFM images.

Source: Voigt et al. [49]/with permission of Springer Nature.

Figure 1.8 (a) Schematic illustration of pinching of a target molecule.

Source: Kuzuya et al. [50]/with permission of Springer Nature.

(b) AFM images for streptavidin (SA) pinching by biotinylated DNA pliers. The dominant form of DNA pliers in Mg²⁺ solution before SA addition (left) was a cross. After SA addition (right), DNA pliers selectively pinched one SA tetramer and closed into the parallel closed form. Scale bars 300 nm.

Source: Kuzuya et al. [50]/with permission of Springer Nature.

(c) Mechanochemical sensing in optical tweezers using DNA origami nanostructures. A connected seven‐tile DNA origami with six probes is tethered between two optically trapped beads through dsDNA handles. Each tile has 39.5 nm × 27 nm in dimension. The adjacent tiles are locked (marked 1–6) by an aptamer DNA and its complementary strand. Unlocking of tiles by the target binding to an aptamer lock. (d) Real‐time observation of the target binding events in the constant‐force detection strategy. Upon switching to the target solution, the binding of the target unlocked the tiles, leading to the extension jumps (arrowheads).

Source: Koirala et al. [51]/with permission of John Wiley & Sons, Inc.