Investigations of storage stability for DNA origami in water and defect analysis

In recent years, the DNA origami technology has been established as a new method of nano surface structuring and patterning. The technology utilizes a long circular scaffold and multiple short staple strands, which can be individually modified resulting in spatial addressability of 2-5 nm [1]. The ability to create highly customizable nanoscale architectures aligns seamlessly with the demands of modern smart system design, where miniaturization and precision are critical, making DNA origami a very promising technology for e.g., lithography [1,2,3]. Despite its promise, the broader application of DNA origami in smart systems is hindered by challenges related to structural stability under practical conditions. Buffer composition and storage conditions are two parameters, which can influence integrity of the DNA origami structures [4,5]. Negative influences on the structural stability can occur in multiples ways, such as misfolded structures, distortion, opening up as well as falling apart of the frame structure. While misfolding mainly happens during the assembly step, the other structural instabilities occur during storage. To address this gap, we systematically investigated key factors influencing the stability of DNA origami assemblies, with a focus on their potential integration into smart micro- and nanoscale devices. In this paper, we investigate the storage stability of our "Frame" structure in PBS buffer supplemented with 10 mM MgCl2 over a time period of 9 weeks. This represents the first stability study for DNA Origami structures in PBS buffered solutions. Furthermore, three distinct design-specific mechanisms of structural degradation were observed and ranked by frequency of occurrence, as well as a best before date of 4 weeks after assembly was determined for the "Frame" structure. For two of these mechanisms, a correlation of simulation data to storage data was found. Based on our results, we have defined four key performance indicators to evaluate the stability of DNA origami structures.