Atomic force microscopy (AFM) is used for high-resolution characterization of DNA nanoparticle structure. AFM measures the surface topography of DNA nanostructures by 'feeling' the nanostructures with an ultrafine tip (nanometer scale). AFM is capable of achieving subnanometer lateral and vertical resolution, rendering it immensely powerful for obtaining single-molecule images of nanostructures.
AFM can image DNA nanostructures in dry or aqueous environments (including in the origami's native buffer). Typically, AFM in liquid achieves higher resolution of DNA nanostructures. However, AFM requires the nanostructure to be adsorbed onto the surface (typically mica or glass) so the nanostructure's state may be biased due to surface interactions1. Interactions between the nanostructure and the cantilever can also cause damage to the structure which can make it challenging to distinguish misformed structures from well-formed structures damaged by the AFM. AFM is not susceptible to staining artifacts and can provide 3D information, two advantages when compared to negative-stain transmission electron microscopy (TEM). However, AFM can distort the dimensions of DNA nanostructures due to edge effects2, making it sometimes less powerful than TEM for accurately measuring the 2D dimensions of a nanostructure.
AFM can also be used to monitor real-time dynamic changes using high-speed AFM (HS-AFM) and to measure mechanical properties of the nanostructure using force spectroscopy.
References
- Wei, B. et al. Design Space for Complex DNA Structures. J. Am. Chem. Soc. 135, 18080–18088 (2013).
- Kolbeck, P. J. et al. DNA Origami Fiducial for Accurate 3D Atomic Force Microscopy Imaging. Nano Lett. 23, 1236–1243 (2023).