DNA origami Nanotechnology for the Visualization, Analysis, and Control of Molecular Events with Nanoscale Precision

Direct visualization of biomolecules of interest allows the elucidation of the physical properties of individual molecules and their reaction processes. Atomic force microscopy (AFM) enables the direct imaging of biomolecules in solution. Since AFM allows visualization of molecules at a nanometer-scale spatial resolution, a versatile observation platform is needed for the precise imaging of molecules in a dynamic state. We used the DNA origami technology for visualizing the detailed movement of target molecules in reactions by using high-speed AFM (HS-AFM), which enables the analysis of the dynamic movement of biomolecules at subsecond time resolution. The conformational changes in DNA molecules, which include noncanonical structures such as formation or disruption of G-quadruplex, i-motif and triplex, and B–Z transition were visualized by combining DNA origami technology and HS-AFM. Enzyme-based reactions such as DNA methylation, excision repair, and recombination were also visualized using this combined observation system and were regulated in the DNA origami frame by imposing structural stress and rotational regulation on substrate DNAs to elucidate the reaction mechanism. Artificial systems responsive to light, metal ions, and specific molecules were constructed and their movements were visualized at single-molecule resolution. These target-orientated observation systems could contribute to a detailed analysis of the motions of biomolecules and elucidation of the mechanism of reactions in real time at molecular resolution.