Molecular self-assembly has become a well-established technique to design complex nanostructures and hierarchical mesoscale assemblies. The typical approach is to design binding complementarity into ...nucleotide or amino acid sequences to achieve the desired final geometry. However, with an increasing interest in dynamic nanodevices, the need to design structures with motion has necessitated the development of multi-component structures. While this has been achieved through hierarchical assembly of similar structural units, here we focus on the assembly of topologically complex structures, specifically with concentric components, where post-folding assembly is not feasible. We exploit the ability to direct folding pathways to program the sequence of assembly and present a novel approach of designing the strand topology of intermediate folding states to program the topology of the final structure, in this case a DNA origami slider structure that functions much like a piston-cylinder assembly in an engine. The ability to program the sequence and control orientation and topology of multi-component DNA origami nanostructures provides a foundation for a new class of structures with internal and external moving parts and complex scaffold topology. Furthermore, this work provides critical insight to guide the design of intermediate states along a DNA origami folding pathway and to further understand the details of DNA origami self-assembly to more broadly control folding states and landscapes.
Efficient self‐assembly: Self‐assembly of DNA nanostructures at room temperature was achieved by incubating the component strands in the presence of a denaturing agent (30–40% formamide). This ...isothermal method is efficient for assembly of both DNA origami (purple, see scheme) and single‐stranded tile (SST, blue) structures, as well as an SST ribbon growing on an origami template.
Dynamic methods of biosensing based on electrical actuation of surface-tethered nanolevers require the use of levers whose movement in ionic liquids is well controllable and stable. In particular, ...mechanical integrity of the nanolevers in a wide range of ionic strengths will enable to meet the chemical conditions of a large variety of applications where the specific binding of biomolecular analytes is analyzed. Herein, we study the electrically induced switching behavior of different rodlike DNA origami nanolevers and compare to the actuation of simply double-stranded DNA nanolevers. Our measurements reveal a significantly stronger response of the DNA origami to switching of electrode potential, leading to a smaller potential change necessary to actuate the origami and subsequently to a long-term stable movement. Dynamic measurements in buffer solutions with different Mg2+ contents show that the levers do not disintegrate even at very low ion concentrations and constant switching stress and thus provide stable actuation performance. The latter will pave the way for many new applications without largely restricting application-specific environments.
Recently developed synthetic membrane pores composed of folded DNA enrich the current range of natural and engineered protein pores and of nonbiogenic channels. Here we report all-atom molecular ...dynamics simulations of a DNA nanotube (DNT) pore scaffold to gain fundamental insight into its atomic structure, dynamics, and interactions with ions and water. Our multiple simulations of models of DNTs that are composed of a six-duplex bundle lead to a coherent description. The central tube lumen adopts a cylindrical shape while the mouth regions at the two DNT openings undergo gating-like motions which provide a possible molecular explanation of a lower conductance state observed in our previous experimental study on a membrane-spanning version of the DNT (ACS Nano 2015, 9, 1117–26). Similarly, the central nanotube lumen is filled with water and ions characterized by bulk diffusion coefficients while the gating regions exhibit temporal fluctuations in their aqueous volume. We furthermore observe that the porous nature of the walls allows lateral leakage of ions and water. This study will benefit rational design of DNA nanopores of enhanced stability of relevance for sensing applications, of nanodevices with tunable gating properties that mimic gated ion channels, or of nanopores featuring defined permeation behavior.
DNA nanotechnology holds great promise for the fabrication of novel plasmonic nanostructures and the potential to carry out single-molecule measurements using optical spectroscopy. Here, we ...demonstrate for the first time that DNA origami nanostructures can be exploited as substrates for surface-enhanced Raman scattering (SERS). Gold nanoparticles (AuNPs) have been arranged into dimers to create intense Raman scattering hot spots in the interparticle gaps. AuNPs (15 nm) covered with TAMRA-modified DNA have been placed at a nominal distance of 25 nm to demonstrate the formation of Raman hot spots. To control the plasmonic coupling between the nanoparticles and thus the field enhancement in the hot spot, the size of AuNPs has been varied from 5 to 28 nm by electroless Au deposition. By the precise positioning of a specific number of TAMRA molecules in these hot spots, SERS with the highest sensitivity down to the few-molecule level is obtained.
A square bipyramidal DNA nanocapsule (NC) was designed to create a nanomaterial carrier. A photocontrollable open/close system and toehold system were introduced into the NC for capture and release ...of a gold nanoparticle (AuNP) by photoirradiation and strand displacement. The inclusion and release of the AuNP was successfully achieved by opening of the NC and strand displacement. The reversible open and closed states were examined by gel electrophoresis and atomic force microscopy. The encapsulation of the AuNP was achieved by hybridization of a specific DNA strand and its release was successfully carried out by opening of the NC and strand displacement. For more details, see the Communication by M. Endo, H. Sugiyama et al. on
This study focused on exploring the ability of self‐assembled DNA frameworks to cross the blood‐brain barrier (BBB). We designed and assembled a series of DNA origami structures with equal quantity ...of nucleic acid materials but different morphologies and rigidities, such as barrel, soccer ball, icosahedron, and compared their transport efficiency in an in vitro BBB model. It was observed that the relatively large and soft structures could better penetrate the BBB through a lysosome irrelative transcytosis process, while the smallest and most rigid structure was blocked severally accompanied with an obvious lysosome digestion once internalized by the endothelial cells.
Three framework DNA origami structures with equal molecular weight but different shape, size and rigidity were compared in parallel to investigate their penetration behaviors cross an artificial blood‐brain barrier and potential mechanisms.
DNA origami technology enables the folding of DNA strands into complex nanoscale shapes whose properties and interactions with molecular species often deviate significantly from that of genomic DNA. ...Here, we investigate the salting-out of different DNA origami shapes by the kosmotropic salt ammonium sulfate that is routinely employed in protein precipitation. We find that centrifugation in the presence of 3 M ammonium sulfate results in notable precipitation of DNA origami nanostructures but not of double-stranded genomic DNA. The precipitated DNA origami nanostructures can be resuspended in ammonium sulfate-free buffer without apparent formation of aggregates or loss of structural integrity. Even though quasi-1D six-helix bundle DNA origami are slightly less susceptible toward salting-out than more compact DNA origami triangles and 24-helix bundles, precipitation and recovery yields appear to be mostly independent of DNA origami shape and superstructure. Exploiting the specificity of ammonium sulfate salting-out for DNA origami nanostructures, we further apply this method to separate DNA origami triangles from genomic DNA fragments in a complex mixture. Our results thus demonstrate the possibility of concentrating and purifying DNA origami nanostructures by ammonium sulfate-induced salting-out.
DNA nanotechnology allows for the realization of complex nanoarchitectures in which the spatial arrangements of different constituents and most functions can be enabled by DNA. When optically active ...components are integrated in such systems, the resulting nanoarchitectures not only provide great insights into the self-assembly of nanoscale elements in a systematic way but also impart tailored optical functionality to DNA origami. In this Letter, we demonstrate DNA-assembled multilayer nanosystems, which can carry out coordinated and reversible sliding motion powered by DNA fuels. Gold nanoparticles cross-link DNA origami filaments to define the configurations of the multilayer nanoarchitectures as well as to mediate relative sliding between the neighboring origami filaments. Meanwhile, the gold nanoparticles serve as optical probes to dynamically interact with the fluorophores tethered on the filaments, rendering in situ detection of the stepwise sliding processes possible. This work seeds the basis to implement DNA-assembled complex optical nanoarchitectures with programmability and addressability, advancing the field with new momentum.
A photofunctionalized square bipyramidal DNA nanocapsule (NC) was designed and prepared for the creation of a nanomaterial carrier. Photocontrollable open/close system and toehold system were ...introduced into the NC for the inclusion and release of a gold nanoparticle (AuNP) by photoirradiation and strand displacement. The reversible open and closed states were examined by gel electrophoresis and atomic force microscopy (AFM), and the open behavior was directly observed by high‐speed AFM. The encapsulation of the DNA‐modified AuNP within the NC was carried out by hybridization of a specific DNA strand (capture strand), and the release of the AuNP was examined by addition of toehold‐containing complementary DNA strand (release strand). The release of the AuNP from the NC was achieved by the opening of the NC and subsequent strand displacement.
An open and shut case: A square bipyramidal DNA nanocapsule (NC) was designed to create a nanomaterial carrier. A photocontrollable open/close system and toehold system were introduced into the NC for capture and release of a gold nanoparticle (AuNP) by photoirradiation and strand displacement. The encapsulation and release of the AuNP was successfully carried out by opening of the NC and strand displacement.
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