Imaging of Unstained DNA Origami Triangles with Electron Microscopy

Imaging of scaffolded DNA and DNA origami nanostructures has been dominated by atomic force microscopy of samples immobilized on bulk substrates. Less commonly used for DNA imaging are electron microscopy techniques, which are typically carried out either after negative staining of DNA or by direct imaging using a bright field cryo-TEM. Here, direct imaging of unstained DNA origami nanostructures on thin electron-transparent substrates utilizing high angular annular dark field scanning transmission electron microscopy )(HAADFSTEM) is reported. This approach establishes a simple method for depositing and imaging intact DNA triangles with mass-thickness contrast, sufficient to measure the scaffold-to-scaffold distances and the length of the triangle’s seam. The signal-to-noise ratio (SNR) of the DNA supported on amorphous carbon as a function of the carbon thickness is measured on three types of commercially available TEM grids to analyze the image resolution. This allows for an edge detection of ~1 nm height DNA triangles on carbon substrates as thick as ~25 nm. 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. Our work presents proof-of-concept results demonstrating that electron microscopy can be utilized to resolve key elements of the DNA origami triangle, without staining or employing exceedingly complicated preparation protocols.