Characterization of 2D material/DNA origami interactions for studies of origami conformational dynamics

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Abstract

The discovery of DNA origami nanotechnology has opened new opportunities in this field due to the versatility of the shapes and sizes that can be generated, the ease of modification and functionalization with molecular resolution, and its biocompatibility. Using Watson-Crick base pairing as the main driver in the self-assembly procedure, DNA origami’s simple assembly process has paved the way for the design of static and dynamic nanostructures. The main methods of characterization are AFM and TEM. While AFM allows the characterization of static and dynamic nanostructures, TEM is only limited to static. However, the TEM’s dynamic imaging ability might be enhanced due to a new technique known as Liquid Cell Electron Microscopy. Graphene, the primary material for the fabrication of Liquid Cells, enables reduced electron scattering, reduced radiation damage and allows enhanced contrast compared to conventional carbon supports. If successful, liquid cell microscopy could enable higher lateral resolution and reduced invasiveness related to AFM measurements while imaging the sample in physiological conditions. However, graphene has been a hostile substrate for DNA origami nanostructures. Due to π−π bonding of graphene, DNA bases react with the delocalized π electrons of graphene and are denatured, causing unwanted deformations in the nanostructures. Additionally, other 2D materials with π −π bonds like MoS2, which was also involved in liquid cell microscopy, have shown similar deformations with DNA origami structures. Various functionalizations have enhanced the biocompatibility of graphene and MoS2 surfaces, reducing the degree of deformation of DNA origami nanostructures. A drawback of all these studies is the lack of similarity between the substrates and the methodologies used for the transfer of 2D materials. This impedes the comparison of the interaction of DNA origami with pristine and functionalized 2D materials. This project aims to qualitatively assess the interaction of DNA origami with pristine and functionalized 2D materials. First, measurements on mica were taken as a baseline for comparison. It was found that the location where the measurement was taken affects the surface’s cleanliness due to the morphology of the cleaved mica. A reduced amount of salt was found present in the centre of the mica compared to the side, which allowed an accurate characterization of DNA origami nanostructures. In addition, rinsing 2-3 times reduced the roughness, increased the adhesion of DNA origami nanostructures and diminished the concentration of salt on the mica substrate. Next, the deposition of DNA origami on graphite substrates has shown a shrinking of DNA origami triangles (≈ 10 nm) due to the melting of dsDNA to ssDNA. A similar deformation was observed in hBN substrates that have a similar shape to graphene but have localized π electrons. Functionalization with poly-l-lysine decreases the degree of deformation of DNA origami nanoarchitectures. However, the values still do not match the ones experienced on mica. Conclusionally, pristine graphite and hBN supports cannot serve as an alternative substrate for imaging DNA origami nanostructures. The optimization of the functionalization protocol might enable the use of graphite as TEM grids.