Quantitative Measurement of Spatial Effects of DNA Origami on Molecular Binding Reactions Detected using Atomic Force Microscopy

DNA origami is a ubiquitous nanostructure that can be used as a universal scaffold for constructing molecular motors, nanosensors, nanodrugs, and optical devices. Understanding the inherent heterogeneity of DNA origami structures is crucial for optimizing the design of high-efficiency nanosized-devices. Here, we investigated the spatial effects of the DNA origami on binding reactions using atomic force microscopy. Protein complexes formed more efficiently at the vertex and rim than on the surface of the DNA origami; surprisingly, the maximum difference in biotin-streptavidin binding efficiency was over 80%, and the change in the binding rate was approximately 40-fold, suggesting the presence of distinct microenvironments at different locations of the DNA origami. Our findings are not only useful for the potential applications of the DNA origami, but also for clarifying differences in nanomaterials caused by nonuniform distribution or defects.