Imaging of Unstained DNA Origami Triangles with Electron Microscopy

Imaging of scaffolded DNA and DNA origami nanostructures has been dominated by atomic force microscopy when the DNA molecules are immobilized on bulk substrates. Less commonly used for DNA imaging are electron microscopy techniques, which are normally carried out either after negative staining of DNA or by direct imaging using a bright field cryo-TEM. Here, we report direct imaging of unstained DNA origami nanostructures on thin electron-transparent substrates by utilizing high angular annular dark field scanning transmission electron microscopy (HAADF-STEM). Our approach establishes a simple method for depositing and imaging of intact DNA triangles with mass-thickness contrast, sufficient to permit identification of the scaffold-to-scaffold distances and the length of the triangle’s seam. We follow the signal-to-noise ratio (SNR) of the DNA supported on amorphous carbon as a function of the carbon thickness in three types of commercially available TEM grids to analyze the image resolution. Accurate edge detection of DNA triangles of ~1 nm height can be achieved on up to 20 nm thick carbon substrates. Additional observations on the effect on SNR with the imaging modes are discussed. The effect of cation concentration used for pre-treating the grid surface on the image resolution is also explored.