Distortion of DNA Origami on Graphene Imaged with Advanced TEM Techniques

Abstract

While graphene may appear to be the ultimate support membrane for transmission electron microscopy (TEM) imaging of DNA nanostructures, very little is known if it poses an advantage over conventional carbon supports in terms of resolution and contrast. Microscopic investigations are carried out on DNA origami nanoplates that are supported onto freestanding graphene, using advanced TEM techniques, including a new dark-field technique that is recently developed in our lab. TEM images of stained and unstained DNA origami are presented with high contrast on both graphene and amorphous carbon membranes. On graphene, the images of the origami plates show severe unwanted distortions, where the rectangular shape of the nanoplates is significantly distorted. From a number of comparative control experiments, it is demonstrated that neither staining agents, nor screening ions, nor the level of electron-beam irradiation cause this distortion. Instead, it is suggested that origami nanoplates are distorted due to hydrophobic interaction of the DNA bases with graphene upon adsorption of the DNA origami nanoplates.

Visualization of unstained homo/heterogeneous DNA nanostructures by low-voltage scanning transmission electron microscopy

“…The Cryo-EM still has a limit in the observation of specific DNA nanostructures with the single image acquisition. Kabiri et al 28 have reported images of the unstained 2D DNA nanostructures on the graphene films with an aberration-corrected TEM at 300 kV. However, unstained nanostructures were almost buried under the background morphology of the graphene supporting film.…”

“…The observation under the high voltage condition caused the small difference in the scattering probabilities of the electrons against the specimen and supporting film. A high angle annular DF detector, which was adopted in the study 28 , further reduces the signal because most of the electrons were scattered into low angles. This explains the low signal-to-background ratio of the images of the unstained DNA origami structures in the previous study 28 .…”

“…A high angle annular DF detector, which was adopted in the study 28 , further reduces the signal because most of the electrons were scattered into low angles. This explains the low signal-to-background ratio of the images of the unstained DNA origami structures in the previous study 28 . Kabiri et al 41 have pursued the issues in their succeeding study.…”

“…For those reasons, direct imaging of unstained DNA nanostructures from a single acquisition has been explored. Kabiri et al 28 have reported the undesirable distortion occurred in 2D DNA nanostructures supported on graphene films through observation of the nanostructures both with and without staining using aberration-corrected scanning transmission electron microscopy (STEM) at 300 keV. Compared with the stained DNA nanostructures on conventional amorphous carbon films, which showed clearer structures with sharp edges, the unstained ones exhibited unclear edges and were buried under the background patterns of the graphene films.…”

Intercalating Electron Dyes for TEM Visualization of DNA at the Single‐Molecule Level

“…Incorporation of these features into the design made it convenient to evaluate if various contrast agents could visualize individual DNA molecules and more extended DNA structures. For details of the origami design and its characterization, we refer to our previous work …”