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DNA Origami Meets AFM: A Promising Duo in Nanoscience

By: Karen Chen, Kaelyn Coates, and Aloha Das

DNA and other similar structures often coil up, obstructing the view of their molecular interactions to researchers. By combining the techniques of AFM (Atomic Force Microscopy) with DNA origami-based scaffolding methods, this paper showcases ways to visualize and study many nanometer-scale common interactions and structures formed by these oligodeoxynucleotides.

DNA origami was employed in various ways in order to control physical aspects such as the tension of strands. One example of this is the use of the DNA Frame that allows DNA strands of different lengths to be attached in order to study the effect of different tensions within the strands. The frame was built with attachments that were able to be swapped out in order to attach varying structures and movements of DNA. AFM allows one to directly observe those biochemical reactions and DNA structural changes in real-time. Combining both processes allows for controlled analysis of processes and features such as DNA methylation, Holliday junctions, hybridizations, G-quadruplexes, helix-handedness, and even DNA-based moving nanomachines. AFMs and HS-AFMs take images over time to study the dynamics of these processes to show how they occur with the help of DNA origami.

AFMs can image almost any surface, which other forms of microscopy cannot. It also includes a non-contact way that does minimal harm to the sample, which reduces issues such as photobleaching, a common issue in biological imaging. Given these methods, it is possible to take high-resolution and high-speed images to characterize many DNA structures that would be otherwise occluded. The advantage of using an AFM to study these structures is being able to image on such a small scale – in comparison to other forms of microscopy such as light microscopes that view cells and organelles. In combination with the DNA Frame keeping the structures in stasis, the processes outlined in this paper enables future experiments with nanomachines or other fast processes.


Endo, Masayuki, and Hiroshi Sugiyama. “Single-Molecule Imaging of Dynamic Motions of Biomolecules in DNA Origami Nanostructures Using High-Speed Atomic Force Microscopy.” Accounts of Chemical Research, vol. 47, no. 6, Mar. 2014,