Search

Technological breakthroughs in cryo-electron microscopy (cryo-EM) methods open new perspectives for highly detailed structural characterizations of extracellular vesicles (EVs) and synthetic liposome–protein assemblies. Structural characterizations of these vesicles in solution under a nearly native hydrated state are of great importance to decipher cell-to-cell communication and to improve EVs’ application as markers in diagnosis and as drug carriers in disease therapy. However, difficulties in preparing holey carbon cryo-EM grids with low vesicle heterogeneities, at low concentration and with kinetic control of the chemical reactions or assembly processes, have limited cryo-EM use in the EV study. We report a straightforward membrane vesicle cryo-EM sample preparation method that assists in circumventing these limitations by using a free-standing DNA-affinity superlattice for covering holey carbon cryo-EM grids. Our approach uses DNA origami to self-assemble to a solution-stable and micrometer-sized ordered molecular template in which structure and functional properties can be rationally controlled. We engineered the template with cholesterol-binding sites to specifically trap membrane vesicles. The advantages of this DNA–cholesterol-affinity lattice (DCAL) include (1) local enrichment of artificial and biological vesicles at low concentration and (2) isolation of heterogeneous cell-derived membrane vesicles (exosomes) from a prepurified pellet of cell culture conditioned medium on the grid.

Technological breakthroughs in electron microscopy (EM) have made it possible to solve structures of biological macromolecular complexes and to raise novel challenges, specifically related to sample preparation and heterogeneous macromolecular assemblies such as DNA–protein, protein–protein, and membrane protein assemblies. Here, we built a V-shaped DNA origami as a scaffolding molecular system to template proteins at user-defined positions in space. This template positions macromolecular assemblies of various sizes, juxtaposes combinations of biomolecules into complex arrangements, isolates biomolecules in their active state, and stabilizes membrane proteins in solution. In addition, the design can be engineered to tune DNA mechanical properties by exerting a controlled piconewton (pN) force on the molecular system and thus adapted to characterize mechanosensitive proteins. The binding site can also be specifically customized to accommodate the protein of interest, either interacting spontaneously with DNA or through directed chemical conjugation, increasing the range of potential targets for single-particle EM investigation. We assessed the applicability for five different proteins. Finally, as a proof of principle, we used RNAP protein to validate the approach and to explore the compatibility of the template with cryo-EM sample preparation.

A comprehensive understanding of the mechanism by which type I collagen (Col) interacts with hydroxyapatite nanoparticles (Hap NPs) in aqueous solutions is a pivotal step for guiding the design of biologically relevant nanocomposites with controlled hierarchical structure. In this paper we use a variety of Hap NPs differing by their shape (rod vs platelet) and their size (∼30 vs ∼130 nm) and investigate their mechanism(s) of interaction with collagen. The addition of collagen to the Hap suspensions induces different effects that strongly depend on the nanoparticle type. Interestingly, the use of small rods, typically with ∼30 nm of length (R30), leads to the formation of assembled collagen fibrils decorated with Hap nanocrystals which, in turn, self-assemble progressively to form larger fibrillar Hap–Col composite. The crystals decorating collagen provide “intrinsic” negative charges to the fibrillar objects that allow their incorporation in three-dimensional structure using layer-by-layer (LbL) assembly. This offers a straightforward way to construct a collagen-based hybrid material with well-defined hierarchy under near-physiological conditions. In situ, QCM-D monitoring revealed the buildup of soft and highly hydrated hybrid (PAH/R30–Col)nmultilayers for which the mechanism of growth was very different from that observed for polyelectrolytes and nanoparticles without collagen (PAH/R30). The LbL assembly of crystal-decorated collagen yields a hierarchical nanostructured film whose thickness and roughness can be modulated by the addition of salt and incorporate fibrillar objects of about 400 nm in width and few micrometers in length, as probed by AFM. The approach described in this work provides a relevant way to better control the (supra)molecular assembly of Col and Hap NPs with the perspective of developing hierarchical Hap–Col nanocomposites with tuned properties for various biomedical applications.