Abstract
DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.
Highlights
During the last three decades, the field of structural DNA nanotechnology has developed a variety of techniques to assemble DNA into increasingly complex nanostructures [1]
This review focuses on the application of atomic force microscopy (AFM) to study molecular processes on DNA origami nanostructures
DNA origami unfolds its real power when the local control of the chemical modifications, i.e., their relative positions, is used to study chemical reactions as a function of distance between the reactants. This was demonstrated by Helmig et al with a photosensitizer placed in the center of a DNA origami rectangle and four singlet oxygen cleavable (SOC) linkers placed at different distances (18 and 36 nm) from the photosensitizer (Figure 4) [25]
Summary
During the last three decades, the field of structural DNA nanotechnology has developed a variety of techniques to assemble DNA into increasingly complex nanostructures [1]. DNA origami templates are frequently used as locally addressable supports (so-called “molecular breadboards”, see Figure 2 left) for the precise arrangement of functional entities such as plasmonic nanoparticles [4,5], quantum dots [6,7], fluorophores [8,9], and proteins [10,11], which enables their use as templates for the study of chemical reactions at a single-molecule level. To detect RNA with a DNA origami and AFM based approach a similar strategy was recently demonstrated using strand displacement reactions and streptavidin (SAv)-quantum dot reporters [23]. This example shows the potential of DNA origami nanostructures to place molecular binding sites with nanometer precision and to study binding events and molecular processes on a nanometer level by AFM.
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