Over the last few years, tremendous progress has been made in visualizing biologically important macromolecules using transmission electron microscopy (TEM) and understanding their structure-function relation. Yet, despite the importance of DNA in all forms of life, TEM visualization of individual DNA molecules in its native unlabeled form has remained extremely challenging. Here, we present high-contrast images of unstained single-layer DNA nanostructures that were obtained using advanced in-focus phase contrast TEM techniques. These include sub-Ångstrom low voltage electron microscopy (SALVE), the use of a volta-potential phase plate (VPP), and dark-field (DF) microscopy. We discuss the advantages and drawbacks of these techniques for broad applications in structural biology and materials science.

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The low contrast of biomolecules in TEM has been a great obstacle for their structure determination and hence to the understanding of their structure-function relation. Historically, single DNA strands remained one the most difficult classes of biomolecular specimens to image, due to low electron scattering strength of its constituent elements. The common practice was then to image them either when freely suspended (without any support) or shadow image them with negative staining technique. Those remedies are limited in terms of applicability to different DNA nanostructures as well as pose difficulties in sample preparation. For example, making the 2D DNA nanostructures freestanding would not be a viable solution for imaging them. This thesis provides a general study to tackle the challenges in imaging nucleic acids with TEM...@en

Staining compounds containing heavy elements (electron dyes) can facilitate the visualization of DNA and related biomolecules by using TEM. However, research into the synthesis and utilization of alternative electron dyes has been limited. Here, we report the synthesis of a novel DNA intercalator molecule, bis-acridine uranyl (BAU). NMR spectroscopy and MS confirmed the validity of the synthetic strategy and gel electrophoresis verified the binding of BAU to DNA. For TEM imaging of DNA, two-dimensional DNA origami nanostructures were used as a robust microscopy test object. By using scanning transmission electron microscopy (STEM) imaging, which is favored over conventional wide-field TEM for improved contrast, and therefore, quantitative image analysis, it is found that the synthesized BAU intercalator can render DNA visible, even at the single-molecule scale. For comparison, other staining compounds with a purported affinity towards DNA, such as dichloroplatinum, cisplatin, osmium tetroxide, and uranyl acetate, have been evaluated. The STEM contrast is discussed in terms of the DNA–dye association constants, number of dye molecules bound per base pair, and the electron-scattering capacity of the metal-containing ligands. These findings pave the way for the future development of electron dyes with specific DNA-binding motifs for high-resolution TEM imaging.

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Osteoporosis is the most widespread metabolic bone disease which represents a major public health burden. Consequently, novel biomaterials with a strong capacity to regenerate osteoporotic bone defects are urgently required. In view of the anti-osteoporotic and osteopromotive efficacy of alendronate and 45S5 bioactive glass, respectively, we investigated the feasibility to synthesize novel hybrid particles by exploiting the strong interactions between these two compounds. Herein, we demonstrate the facile preparation of a novel class of hybrid particles of tunable morphology, chemical composition and structure. These hybrid particles (i) release alendronate and various inorganic elements (Ca, Na, Si, and P) in a controlled manner, (ii) exhibit a strong anti-osteoclastic effect in vitro, and (iii) stimulate regeneration of osteoporotic bone in vivo. Consequently, this novel class of hybrid biomaterials opens up new avenues of research on the design of bone substitutes with specific activity to facilitate regeneration of bone defects in osteoporotic patients.

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The key to understanding the performance of Li–O₂ batteries is to study the chemical and structural properties of their discharge product(s) at the nanometer scale. Using TEM for this purpose poses challenges due to the sensitivity of samples to air and electron beams. This paper describes our use of in situ EELS to evaluate experimental procedures to reduce electron-beam degradation and presents methods to deal with air sensitivity. Our results show that Li₂O₂ decomposition is dependent on the total dose and is approximately 4–5 times more pronounced at 80 than at 200 kV. We also demonstrate the benefits of using low-dose-rate STEM. We show further that a “graphene cell” which encapsulates the sample within graphene sheets, can protect the sample against air and e-beam damage.

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While graphene may appear to be the ultimate support membrane for transmission electron microscopy (TEM) imaging of DNA nanostructures, very little is known if it poses an advantage over conventional carbon supports in terms of resolution and contrast. Microscopic investigations are carried out on DNA origami nanoplates that are supported onto freestanding graphene, using advanced TEM techniques, including a new dark-field technique that is recently developed in our lab. TEM images of stained and unstained DNA origami are presented with high contrast on both graphene and amorphous carbon membranes. On graphene, the images of the origami plates show severe unwanted distortions, where the rectangular shape of the nanoplates is significantly distorted. From a number of comparative control experiments, it is demonstrated that neither staining agents, nor screening ions, nor the level of electron-beam irradiation cause this distortion. Instead, it is suggested that origami nanoplates are distorted due to hydrophobic interaction of the DNA bases with graphene upon adsorption of the DNA origami nanoplates.

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