Many challenges in biosensing originate from the fact that the all-important nanoarchitecture of the biosensor surface, including precise density and orientation of bioreceptors, is not entirely comprehended. Here, we introduced a three-dimensional DNA origami as a bioreceptor carrier to functionalize the fiber optic surface plasmon resonance (FO-SPR) sensor with nanoscale precision. Starting from a 24-helix bundle, two distinct DNA origami structures were designed to position thrombin-specific aptamers with different densities and distances (27 and 113 nm) from the FO-SPR surface. The origami-based biosensors not only proved to be capable of reproducible, label-free thrombin detection but revealed also valuable innovative features: (1) a significantly better performance in the absence of backfilling, known as essential in the biosensing field, suggesting improved bioreceptor orientation and accessibility, and (2) a wider linear range compared to previously reported thrombin biosensors. We envisage that our method will be beneficial for both scientists and clinicians looking for new surface (bio)chemistry and improved diagnostics.
From atoms to molecules and bio-macromolecules, from organelles to cells, tissues, to the whole living system, nature shows us that the formation of complex systems with emergent properties originates from the hierarchical self-assembly of single components in guided bottom-up processes. By using DNA as a fundamental building block with well-known self-recognition properties, scientists have developed design rules and physical-chemical approaches for the fully programmable construction of highly organized structures with nanosized features. This review highlights the basic principles of hierarchical self-assembly in terms of type and number of distinguishable components and their interaction energies. Such general concepts are then applied to DNA-based systems. After a brief overview of the strategies used until now for the construction of individual DNA units, such as DNA tile motifs and origami structures, their self-association into assemblies of higher order is discussed. Particular emphasis is given to the forces involved in the self-assembly process, understanding and rational combination of which might help to coordinate the single elements of hierarchical structures both in space and time, thus advancing our efforts towards the creation of devices that mimic the complexity and functionality of natural systems.
The elastic features of protein filaments are encoded in their component units and in the way they are connected, thus defining a biunivocal relationship between the monomer and the result of its self-assembly. Using DNA origami approaches, we constructed a reconfigurable module, composed of two quasi-independent domains and four possible interfaces, capable of facial and lateral growing through specific recognition patterns. Whereas the flexibility of the intra-domains region can be regulated by switchable DNA motifs, the inter-domain interfaces feature mutually and self-complementary shapes, whose pairwise association leads to filaments of programmable periodicity and variable persistence length. Thus, we show here that the assembly pathway leading to oligomeric chains can be finely tuned and fully controlled, enabling the emulation of protein-like filaments using a single construction principle. Our approach results in artificial materials with a large variety of ultrastructures and bending strengths comparable, or even superior, to their natural counterparts.
The self-assembly of a DNA origami structure, although mostly feasible, represents indeed a rather complex folding problem. Entropy-driven folding and nucleation seeds formation may provide possible solutions; however, until now, a unified view of the energetic factors in play is missing. Here, by analyzing the self-assembly of origami domains with identical structure but different nucleobase composition, in function of variable design and experimental parameters, we identify the role played by sequence-dependent forces at the edges of the structure, where topological constraint is higher. Our data show that the degree of mechanical stress experienced by these regions during initial folding reshapes the energy landscape profile, defining the ratio between two possible global conformations. We thus propose a dynamic model of DNA origami assembly that relies on the capability of the system to escape high structural frustration at nucleation sites, eventually resulting in the emergence of a more favorable but previously hidden state.
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