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Chembiochem. 2019 Jun 4. doi: 10.1002/cbic.201900369. [Epub ahead of print]

Real-Time Observation of Superstructure-Dependent DNA Origami Digestion by DNase I Using High-Speed Atomic Force Microscopy.

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Technical and Macromolecular Chemistry, Paderborn University, Warburger Strasse 100, 33098, Paderborn, Germany.
Present address: Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA.
Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P. O. Box 16100, 00076, Aalto, Finland.
HYBER Center of Excellence, Department of Applied Physics, Aalto University, P. O. Box 16100, 00076, Aalto, Finland.


DNA nanostructures have emerged as intriguing tools for numerous biomedical applications. However, in many of those applications and most notably in drug delivery, their stability and function may be compromised by the biological media. A particularly important issue for medical applications is their interaction with proteins such as endonucleases, which may degrade the well-defined nanoscale shapes. Herein, fundamental insights into this interaction are provided by monitoring DNase I digestion of four structurally distinct DNA origami nanostructures (DONs) in real time and at a single-structure level by using high-speed atomic force microscopy. The effect of the solid-liquid interface on DON digestion is also assessed by comparison with experiments in bulk solution. It is shown that DON digestion is strongly dependent on its superstructure and flexibility and on the local topology of the individual structure.


DNA; DNA origami; endonucleases; high-speed atomic force microscopy; nanotechnology


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