Characterizing the structure of 3D DNA origami in a transmission electron microscope

DNA origami nanostructures provide programmable control over nanoscale geometry but remain challenging to image due to their low atomic number. Here, we systematically evaluate imaging strategies for both stained and unstained DNA origami deposited on carbon-coated TEM grids. Using Weber contrast as a quantitative metric, we compared different operating modes of (scanning) transmission electron microscopy, (S)TEM, in order to find optimum imaging conditions. STEM was consistently found to deliver the highest contrast, with optimal performance at a camera length of 600 mm towards the high angle annular dark field (HAADF) detector. As expected, the contrast was higher for the thicker three-dimensional nanotubes as compared to DNA 6-helix bundles (6HBs) due to the larger projected thickness of the former. The contrast was effectively enhanced by heavy metal staining with uranyl formate. Notably, 3D molds preserved their designated dimensions upon staining and also largely retained their structural integrity upon complexation with palladium, which also improved the visibility of the structures. These results establish STEM as the optimal approach for high-contrast imaging of DNA origami even of unstained samples and provide practical guidelines for sample preparation and imaging conditions that promote reliable structural visualization.