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The reliable programmability of DNA origami makes it an extremely attractive tool for bottom-up self-assembly of complex nanostructures. Utilizing this property for the tuned arrangement of plasmonic nanoparticles holds great promise particularly in the field of biosensing. Plasmonic particles are beneficial for sensing in multiple ways, from enhancing fluorescence to enabling a visualization of the nanoscale dynamic actuation via chiral rearrangements. In this Perspective, we discuss the recent developments and possible future directions of DNA origami-enabled plasmonic sensing systems. We start by discussing recent advancements in the area of fluorescence-based plasmonic sensing using DNA origami. We then move on to surface-enhanced Raman spectroscopy sensors followed by chiral sensing, both utilizing DNA origami nanostructures. We conclude by providing our own views on the future prospects for plasmonic biosensors enabled using DNA origami.

The design of dynamic, reconfigurable devices is crucial for the bottom-up construction of artificial biological systems. DNA can be used as an engineering material for the de-novo design of such dynamic devices. A self-assembled DNA origami switch is presented that uses the transition from double- to single-stranded DNA and vice versa to create and annihilate an entropic force that drives a reversible conformational change inside the switch. It is distinctively demonstrated that a DNA single-strand that is extended with 0.34 nm per nucleotide - the extension this very strand has in the double-stranded configuration - exerts a contractive force on its ends leading to large-scale motion. The operation of this type of switch is demonstrated via transmission electron microscopy, DNA-PAINT super-resolution microscopy and darkfield microscopy. The work illustrates the intricate and sometimes counter-intuitive forces that act in nanoscale physical systems that operate in fluids.

Over the past few decades, DNA has turned into one of the most widely used molecular linkers and a versatile building block for the self-assembly of DNA nanostructures. Such complexes, composed of only a few oligonucleotides (e.g., DNA tiles) or assembled from hundreds of synthetic and natural scaffolding strands (e.g., DNA origami), are being increasingly assembled into higher-order architectures such as lattices and crystals. A wide variety of assembly methods and techniques (e.g., solution-phase and substrate-assisted sticky-ended cohesion or blunt-end stacking) have emerged and are constantly being refined. This review provides a summary of the methods and building blocks for the assembly of 2D and 3D DNA lattices and crystals, and discusses some of their potential applications in materials science.

Recent developments in DNA nanotechnology brought rich structural and functional diversity. However, for DNA nanostructures to perform in a biologically relevant context, obstacles such as nuclease activity and low divalent ion concentrations have to be addressed. For drug delivery or gene therapy applications, ultimately the lipid membrane barriers must be targeted and overcome. In this article, we highlight efforts and achievements in enhancing the stability of DNA nanostructures including chemical modifications, covalent crosslinking and coating with protective layers composed of polymers or lipids. We then review interactions between DNA nanostructures and lipid membranes, which are often mediated by ligands for membrane receptors or hydrophobic domains incorporated into the structure. Finally, we present applications of DNA nanostructures on and in lipid membranes, including higher order assembly, controlling membrane curvature, targeting and arranging membrane proteins in living cells and DNA-based synthetic lipid channels.

Molecular recognition, which is key to the correct functioning of most biological processes, is based on chiral entities fitting into and onto each other. Consequently, the concept of chirality appears virtually everywhere in biology and biochemistry. One striking optical manifestation of the chirality of biomolecules is circular dichroism (CD), which is very typical for biorelated systems. It has been demonstrated over the past decade that bioassembled plasmonic nanostructures offer amazing possibilities regarding chirality and optical responses, and the active research field of chiral bioplasmonics has recently generated a variety of new sensing platforms. In both molecular and nanoscale systems, optical manifestations of chirality arise from complex interactions between nonchiral elements. Such interactions decay rapidly with the distance between the elements, and therefore, a system with strong optical chiral responses typically is tightly packed. Here we show how to transfer chiral interactions effic...

Cell signaling is initiated by characteristic protein patterns in the plasma membrane, but tools to decipher their molecular organization and activation are hitherto lacking. Among the well-known signaling pattern is the death inducing signaling complex with a predicted hexagonal receptor architecture. To probe this architecture, DNA origami-based nanoagents with nanometer precise arrangements of the death receptor ligand FasL are introduced and presented to cells. Mimicking different receptor geometries, these nanoagents act as signaling platforms inducing fastest time-to-death kinetics for hexagonal FasL arrangements with 10 nm inter-molecular spacing. Compared to naturally occurring soluble FasL, this trigger is faster and 100x more efficient. Nanoagents with different spacing, lower FasL number or higher coupling flexibility impede signaling. The results present DNA origami as versatile signaling scaffolds exhibiting unprecedented control over molecular number and geometry. They define molecular benchmarks in apoptosis signal initiation and constitute a new strategy to drive particular cell responses.

International audience; Synthetic biomimetic microswimmers are promising agents for in vivo healthcare and important frameworks to advance the understanding of locomotion strategies and collective motion at the microscopic scale. Nevertheless, constructing these devices with design flexibility and in large numbers remains a challenge. Here, a step toward meeting this challenge is taken by assembling such swimmers via the programmed shape and arrangement of superparamagnetic micromodules. The method's capacity for design flexibility is demonstrated through the assembly of a variety of swimmer architectures. On their actuation, strokes characterized by a balance of viscous and magnetic forces are found in all cases, but swimmers formed from a series of size‐graded triangular modules swim quicker than more traditional designs comprising a circular “head” and a slender tail. Linking performance to design, rules are extracted informing the construction of a second‐generation swimmer with a short tail and an elongated head optimized for speed. Its fast locomotion is attributed to a stroke that better breaks beating symmetry and an ability to beat fully with flex at high frequencies. Finally, production at scale is demonstrated through the assembly and swimming of a flock of the triangle‐based architectures to reveal four types of swimmer couplings.

The spatial organization of metal nanoparticles has become an important tool for manipulating light in nanophotonic applications. Silver nanoparticles, particularly silver nanorods, have excellent plasmonic properties but are prone to oxidation and are therefore inherently unstable in aqueous solutions and salt-containing buffers. Consequently, gold nanoparticles have often been favored, despite their inferior optical performance. Bimetallic, i.e., gold-silver core-shell nanoparticles, can resolve this issue. We present a method for synthesizing highly stable gold-silver core-shell NRs that are instantaneously functionalized with DNA, enabling chiral self-assembly on DNA origami. The silver shell gives rise to an enhancement of plasmonic properties, reflected here in strongly increased circular dichroism, as compared to pristine gold nanorods. Gold-silver nanorods are ideal candidates for plasmonic sensing with increased sensitivity as needed in pathogen RNA or antibody testing for nonlinear optics and light-funneling applications in surface enhanced Raman spectroscopy. Furthermore, the control of interparticle orientation enables the study of plasmonic phenomena, in particular, synergistic effects arising from plasmonic coupling of such bimetallic systems.

International audience; Plasmonic materials are intensively used to extend the photoactivity of large bandgap semiconductors into the visible light region. In this framework, the present study examines the joint role played by the morphology and composition of plasmonic nano-particles in their photosensitizing capabilities. The critical influence of these parameters is evidenced by the effect of Au and core−shell Au@Ag nanorods on a TiO 2-driven photochemical probe reaction. In this case, the use of the bimetallic composites leads to a remarkable increase in the photocatalytic activity of the semiconductor compared to that found for the monometallic Au sensitizers. The mechanism behind this observation has then been computed theoretically concluding that, in terms of hot electron injection, the contribution of the transversal modes of the Au@Ag NRs and the low damping of these nanostructures are responsible for the photocatalytic properties reported herein. The great potential of these architectures is confirmed by their notable performance toward photocatalytic hydrogen generation, rendering this approach an appealing strategy in the search for efficient solar-driven energy systems. N oble metal nanoparticles (NPs) present outstanding optical properties given their strong interaction with light in the visible and near-infrared (NIR) ranges of the electromagnetic spectrum. 1 This coupling arises because of the coherent oscillation of conduction electrons of the metallic objects in resonance with the incoming electromagnetic field, an effect known as localized surface plasmon resonance (LSPR). 2 As a result, a short-lived population of charge carriers ("hot" electrons) is created, being thermalized within the crystalline lattice of the metal on the femtosecond time scale. 3,4 Recent reports have shown that the combination of plasmonic objects with acceptor species such as organic molecules or semiconductors can lead to the exchange of charge carriers and hence to the possibility of using such species to drive chemical processes of interest. 5 Along these lines, plasmonic photosensitization has been identified as a promising interaction between a noble metal and a large bandgap semiconductor toward the formation of hybrid photocatalysts with improved efficiencies and broadband activity. 6,7 In this manner, the Schottky barrier created between both materials extends the lifetime of the hot carriers, thus leading to an accumulation of electrons at the conduction band

The interaction between light and matter can be controlled efficiently by structuring materials at a length scale shorter than the wavelength of interest. With the goal to build optical devices that operate at the nanoscale, plasmonics has established itself as a discipline, where near-field effects of electromagnetic waves created in the vicinity of metallic surfaces can give rise to a variety of novel phenomena and fascinating applications. As research on plasmonics has emerged from the optics and solid-state communities, most laboratories employ top-down lithography to implement their nanophotonic designs. In this review, we discuss the recent, successful efforts of employing self-assembled DNA nanostructures as scaffolds for creating advanced plasmonic architectures. DNA self-assembly exploits the base-pairing specificity of nucleic acid sequences and allows for the nanometer-precise organization of organic molecules but also for the arrangement of inorganic particles in space. Bottom-up self-assembly thus bypasses many of the limitations of conventional fabrication methods. As a consequence, powerful tools such as DNA origami have pushed the boundaries of nanophotonics and new ways of thinking about plasmonic designs are on the rise.

Elaborating efficient strategies and deepening the understanding of light transport at the nanoscale is of great importance for future designs of artificial light-harvesting assemblies and dye-based photonic circuits. In this work, we focus on studying the phenomenon of Förster resonance energy transfer (FRET) among fluorophores of the same kind (homo-FRET) and its implications for energy cascades containing two or three different dye molecules. Utilizing the spatial programmability of DNA origami, we arranged a chain of cyanine 3 (Cy3) dyes flanked at one end with a dye of lower excitation energy, cyanine 5 (Cy5), with or without an additional dye of higher excitation energy, Alexa488, at the other end. We characterized the response of our fluorophore assemblies with bulk and single-molecule spectroscopy and support our measurements by Monte Carlo modeling of energy transfer within the system. We find that, depending on the arrangement of the fluorophores, homo-FRET between the Cy3 dyes can lead to an overall enhanced energy transfer to the acceptor fluorophore. Furthermore, we systematically analyzed the homo-FRET system by addressing the fluorescence lifetime and anisotropy. Finally, we built a homo-FRET-mediated photonic wire capable of transferring energy through the homo-FRET system from the blue donor dye (Alexa488) to the red acceptor fluorophore (Cy5) across a total distance of 16 nm.

Precious metals and liquid crystals (LC) are quite different yet share some common features, for example, their beauty, distinguished optical properties and a competition of high prices per gramme. Triggered by the vision of artificial materials with extremely unusual properties (metamaterials), facilitated by the methods of modern nanotechnology and motivated by John Goodby’s and other colleagues’ synthetic activities, combinations of LCs and gold nanoparticles or nanostructures have attracted much attention during the last decade. This noncomprehensive article describes some examples and insights in this field. Perspectives and opportunities of further research are discussed.

Although DNA origami nanostructures have found their way into numerous fields of fundamental and applied research, they often suffer from rather limited stability when subjected to environments that differ from the employed assembly conditions, that is, suspended in Mg2+ -containing buffer at moderate temperatures. Here, means for efficient cryopreservation of 2D and 3D DNA origami nanostructures and, in particular, the effect of repeated freezing and thawing cycles are investigated. It is found that, while the 2D DNA origami nanostructures maintain their structural integrity over at least 32 freeze-thaw cycles, ice crystal formation makes the DNA origami gradually more sensitive toward harsh sample treatment conditions. Whereas no freeze damage could be detected in 3D DNA origami nanostructures subjected to 32 freeze-thaw cycles, 1000 freeze-thaw cycles result in significant fragmentation. The cryoprotectants glycerol and trehalose are found to efficiently protect the DNA origami nanostructures against freeze damage at concentrations between 0.2 × 10-3 and 200 × 10-3 m and without any negative effects on DNA origami shape. This work thus provides a basis for the long-term storage of DNA origami nanostructures, which is an important prerequisite for various technological and medical applications.

We demonstrate the capability of DNA selfassembledoptical antennas to direct the emission of anindividual fluorophore, which is free to rotate. DNA origami isused to fabricate optical antennas composed of two colloidalgold nanoparticles separated by a predefined gap and to place asingle Cy5 fluorophore near the gap center. Although thefluorophore is able to rotate, its excitation and far-field emissionis mediated by the antenna, with the emission directionalityfollowing a dipolar pattern according to the antenna mainresonant mode. This work is intended to set out the basis formanipulating the emission pattern of single molecules with selfassembledoptical antennas based on colloidal nanoparticles. Fil: Hübner, Kristina. Universidad de Múnich; Alemania Fil: Pilo-Pais, Mauricio. Fribourg University; Suiza Fil: Selbach, Florian. Universidad de Múnich; Alemania Fil: Liedl, Tim. Universidad de Múnich; Alemania Fil: Tinnefeld, Philip. Universidad de Múnich; Alemania Fil: Stefani, Fernando Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Bionanociencias "Elizabeth Jares Erijman"; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina Fil: Acuna, Guillermo P.. Fribourg University; Suiza

DNA nanotechnology offers the possibility to rationally design structures with emergent properties by precisely controlling their geometry and functionality. Here, we demonstrate a DNA-based plasmonic metamolecule that is capable of sensing human thrombin proteins. The chiral reconfigurability of a DNA origami structure carrying two gold nanorods was used to provide optical read-out of thrombin binding through changes in the displayed plasmonic circular dichroism. In our experiments, each arm of the structure was modified with one of two different thrombin-binding aptamers&mdash, thrombin-binding aptamer (TBA) and HD22&mdash, in such a way that a thrombin molecule could be sandwiched by the aptamers to lock the metamolecule in a state of defined chirality. Our structure exhibited a Kd of 1.4 nM, which was an order of magnitude lower than those of the individual aptamers. The increased sensitivity arose from the avidity gained by the cooperative binding of the two aptamers, which was also reflected by a Hill coefficient of 1.3 &plusmn, 0.3. As we further exploited the strong plasmonic circular dichroism (CD) signals of the metamolecule, our method allowed one-step, high sensitivity optical detection of human thrombin proteins in solution.

DNA nanotechnology has developed into a state where the design and assembly of complex nanoscale structures has become fast, reliable, cost-effective, and accessible to non-experts. Nanometer-precise positioning of organic (dyes, biomolecules, etc.) and inorganic (metal nanoparticles, colloidal quantum dots, etc.) components on DNA nanostructures is straightforward and modular. In this perspective article, we identify the opportunities and challenges that DNA-assembled devices and materials are facing for optical antennas, metamaterials, and sensing applications. With the abilities of arranging hybrid materials in defined geometries, plasmonic effects will, for example, amplify molecular recognition transduction so that single-molecule events will be measureable with simple devices. On the larger scale, DNA nanotechnology has the potential of breaking the symmetry of common self-assembled functional materials creating pre-defined optical properties such as refractive index tuning, Bragg reflection and topological insulation.

DNA nanostructures offer the possibility to mimic functional biological membrane components due to their nanometer-precise shape configurability and versatile biochemical functionality. Here we show that the diffusional behavior of DNA nanostructures and their assembly into higher order membrane-bound lattices can be controlled in a stop-and-go manner and that the process can be monitored with super-resolution imaging. The DNA structures are transiently immobilized on glass-supported lipid bilayers by changing the mono- and divalent cation concentrations of the surrounding buffer. Using DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) super-resolution microscopy, we confirm the fixation of DNA origami structures with different shapes. On mica-supported lipid bilayers, in contrast, we observe residual movement. By increasing the concentration of NaCl and depleting MgCl2, a large fraction of DNA structures restarts to diffuse freely on both substrates. After addition of a set of oligonucleotides that enables three Y-shaped monomers to assemble into a three-legged shape (triskelion), the triskelions can be stopped and super-resolved. Exchanging buffer and adding another set of oligonucleotides triggers the triskelions to diffuse and assemble into hexagonal 2D lattices. This stop-and-go imaging technique provides a way to control and observe the diffusional behavior of DNA nanostructures on lipid membranes that could also lead to control of membrane-associated cargos.

The use of biomaterials, with techniques such as DNA-directed assembly or biodirected synthesis, can surpass top-down fabrication techniques in creating plasmonic superstructures in terms of spatial resolution, range of functionality, and fabrication speed. In particular, by enabling a very precise placement of nanoparticles in a bioassembled complex or through the controlled biodirected shaping of single nanoparticles, plasmonic nanocrystals can show remarkably strong circular dichroism (CD) signals. We show that chiral bioplasmonic assemblies and single nanocrystals can enable polarization-sensitive photochemistry based on the generation of energetic (hot) electrons. It is now established that hot plasmonic electrons can induce surface photochemistry or even reshape plasmonic nanocrystals. We show that merging chiral plasmonic nanocrystal systems and the hot-election generation effect offers unique possibilities in photochemistry, such as polarization-sensitive photochemistry promoting nonchiral molecular reactions, chiral photoinduced growth of a colloid at the atomic level, and chiral photochemical destruction of chiral nanocrystals. In contrast, for chiral molecular systems, the equivalent of the described effects is challenging to observe because molecular species typically exhibit very small CD signals. Moreover, we compare our findings with traditional chiral photochemistry at the molecular level, identifying new, different regimes for chiral photochemistry with possibilities that are unique for plasmonic colloidal systems. In this study, we bring together the concept of hot-electron generation and the field of chiral colloidal plasmonics. Using chiral plasmonic nanorod complexes as a model system, we demonstrate remarkably strong CD in both optical extinction and generation rates of hot electrons. Studying the regime of steady-state excitation, we discuss the influence of geometrical and material parameters on the chiral effects involved in the generation of hot electrons. Optical chirality and the chiral hot-electron response in the nanorod dimers result from complex interparticle interactions, which can appear in the weak coupling regime or in the form of Rabi splitting. Regarding practical applications, our study suggests interesting opportunities in polarization-sensitive photochemistry, in chiral recognition or separation, and in promoting chiral crystal growth at the nanoscale.

The chiral state of a molecule plays a crucial role in molecular recognition and biochemical reactions. Because of this and owing to the fact that most modern drugs are chiral, the sensitive and reliable detection of the chirality of molecules is of great interest to drug development. The majority of naturally occurring biomolecules exhibit circular dichroism (CD) in the UV range. Theoretical studies and several experiments have demonstrated that this UV-CD can be transferred into the plasmonic frequency domain when metal surfaces and chiral biomolecules are in close proximity. Here, we demonstrate that the CD transfer effect can be drastically enhanced by placing chiral molecules, here double-stranded DNA, inside a plasmonic hotspot. By using different particle types (gold, silver, spheres, and rods) and by exploiting the versatility of DNA origami, we were able to systematically study the impact of varying particle distances on the CD transfer efficiency and to demonstrate CD transfer over the whole optical spectrum down to the near-infrared. For this purpose, nanorods were also placed upright on DNA origami sheets, forming strong optical antennas. Theoretical models, demonstrating the intricate relationships between molecular chirality and achiral electric fields, support our experimental findings. From both experimental measurements and theoretical considerations, we conclude that the transferred CD is most intensive for systems with strong plasmonic hotspots, as we find them in relatively small gaps (5-12 nm) between spherical nanoparticles and preferably between the tips of nanorods.

Composites of DNA origami nanostructures dispersed in a lyotropic chromonic liquid crystal are studied by polarizing optical microscopy. The homogeneous aqueous dispersions can be uniformly aligned by confinement between two glass substrates, either parallel to the substrates owing to uniaxial rubbing or perpendicular to the substrates using ozonized graphene layers. These opportunities of uniform alignment may pave the way for tailored anisometric plasmonic DNA nanostructures to photonic materials. In addition, a decorated texture with nonuniform orientation is observed on substrates coated with pristine graphene. When the water is allowed to evaporate slowly, microscopic crystal needles appear, which are aligned along the local orientation of the director. This decoration method can be used for studying the local orientational order and the defects in chromonic liquid crystals.

We show that DNA-based self-assembly can serve as a general and flexible tool to construct artificial flagella of several micrometers in length and only tens of nanometers in diameter. By attaching the DNA flagella to biocompatible magnetic microparticles, we provide a proof of concept demonstration of hybrid structures that, when rotated in an external magnetic field, propel by means of a flagellar bundle, similar to self-propelling peritrichous bacteria. Our theoretical analysis predicts that flagellar bundles that possess a length-dependent bending stiffness should exhibit a superior swimming speed compared to swimmers with a single appendage. The DNA self-assembly method permits the realization of these improved flagellar bundles in good agreement with our quantitative model. DNA flagella with well-controlled shape could fundamentally increase the functionality of fully biocompatible nanorobots and extend the scope and complexity of active materials.

A wide variety of organic dyes form, under certain conditions, clusters know as J- and H-aggregates. Cyanine dyes are such a class of molecules where the spatial proximity of several dyes leads to overlapping electron orbitals and thus to the creation of a new energy landscape compared to that of the individual units. In this work, we create artificial H-aggregates of exactly two Cyanine 3 (Cy3) dyes by covalently linking them to a DNA molecule with controlled subnanometer distances. The absorption spectra of these coupled systems exhibit a blue-shifted peak, whose intensity varies depending on the distance between the dyes and the rigidity of the DNA template. Simulated vibrational resolved spectra, based on molecular orbital theory, excellently reproduce the experimentally observed features. Circular dichroism spectroscopy additionally reveals distinct signals, which indicates a chiral arrangement of the dye molecules. Molecular dynamic simulations of a Cy3-Cy3 construct including a 14-base pair DNA sequence verified chiral stacking of the dye molecules.

Rod-like and sheet-like nano-particles made of desoxyribonucleic acid (DNA) fabricated by the DNA origami method (base sequence-controlled self-organized folding of DNA) are dispersed in a lyotropic chromonic liquid crystal made of an aqueous solution of disodium cromoglycate. The respective liquid crystalline nanodispersions are doped with a dichroic fluorescent dye and their orientational order parameter is studied by means of polarized fluorescence spectroscopy. The presence of the nano-particles is found to slightly reduce the orientational order parameter of the nematic mesophase. Nano-rods with a large length/width ratio tend to preserve the orientational order, while more compact stiff nano-rods and especially nano-sheets reduce the order parameter to a larger extent. In spite of the difference between the sizes of the DNA nano-particles and the rod-like columnar aggregates forming the liquid crystal, a similarity between the shapes of the former and the latter seems to be better compatible with the orientational order of the liquid crystal.

Detecting small sequences of RNA in biological samples such as microRNA or viral RNA demands highly sensitive and specific methods. Here, a reconfigurable DNA origami template has been used where a chiral arrangement of gold nanorods on the structure can lead to the generation of strong circular dichroism (CD). Switching of the cross-like DNA structure is achieved by the addition of nucleic acid sequences, which arrests the structure in one of the possible chiral states by specific molecular recognition. A specific sequence can thus be detected through the resulting changes in the plasmonic CD spectrum. We show the sensitive and selective detection of a target RNA sequence from the hepatitis C virus genome. The RNA binds to a complementary sequence that is part of the lock mechanism, which leads to the formation of a defined state of the plasmonic system with a distinct optical response. With this approach, we were able to detect this specific RNA sequence at concentrations as low as 100 pm.

DNA origami objects allow for accurate positioning of guest molecules in three dimensions. Validation and understanding of design strategies for particle attachment as well as analysis of specific particle arrangements are desirable. Small-angle X-ray scattering (SAXS) is suited to probe distances of nano-objects with subnanometer resolution at physiologically relevant conditions including pH and salt and at varying temperatures. Here, we show that the pair density distribution function (PDDF) obtained from an indirect Fourier transform of SAXS intensities in a model-free way allows to investigate prototypical DNA origami-mediated gold nanoparticle (AuNP) assemblies. We analyze the structure of three AuNP-dimers on a DNA origami block, an AuNP trimer constituted by those dimers, and a helical arrangement of nine AuNPs on a DNA origami cylinder. For the dimers, we compare the model-free PDDF and explicit modeling of the SAXS intensity data by superposition of scattering intensities of the scattering objects. The PDDF of the trimer is verified to be a superposition of its dimeric contributions, that is, here AuNP-DNA origami assemblies were used as test boards underlining the validity of the PDDF analysis beyond pairs of AuNPs. We obtain information about AuNP distances with an uncertainty margin of 1.2 nm. This readout accuracy in turn can be used for high precision placement of AuNP by careful design of the AuNP attachment sites on the DNA-structure and by fine-tuning of the connector types.

Forces in biological systems are typically investigated at the single-molecule level with atomic force microscopy or optical and magnetic tweezers, but these techniques suffer from limited data throughput and their requirement for a physical connection to the macroscopic world. We introduce a self-assembled nanoscopic force clamp built from DNA that operates autonomously and allows massive parallelization. Single-stranded DNA sections of an origami structure acted as entropic springs and exerted controlled tension in the low piconewton range on a molecular system, whose conformational transitions were monitored by single-molecule Förster resonance energy transfer. We used the conformer switching of a Holliday junction as a benchmark and studied the TATA-binding protein-induced bending of a DNA duplex under tension. The observed suppression of bending above 10 piconewtons provides further evidence of mechanosensitivity in gene regulation.

Multihelical DNA bundles could enhance the functionality of nanomaterials and serve as model architectures to mimic protein filaments on the molecular and cellular level. We report the self-assembly of micrometer-sized helical DNA nanotubes with widely controllable helical diameters ranging from tens of nanometers to a few micrometers. Nanoscale helical shapes of DNA tile tubes (4-, 6-, 8-, 10-, and 12-helix tile tubes) are achieved by introducing discrete amounts of bending and twist through base pair insertions and/or deletions. Microscale helical diameters, which require smaller amounts of twist and bending, are achieved by controlling the intrinsic “supertwist” present in tile tubes with uneven number of helices (11-, 13-, and 15-helix tile tubes). Supertwist fine-tuning also allows us to produce helical nanotubes of defined chirality.

Plasmonic nanoparticles hold great promise as photon handling elements and as channels for coherent transfer of energy and information in future all-optical computing devices. Coherent energy oscillations between two spatially separated plasmonic entities via a virtual middle state exemplify electron-based population transfer, but their realization requires precise nanoscale positioning of heterogeneous particles. Here, we show the assembly and optical analysis of a triple particle system consisting of two gold nanoparticles with an inter-spaced silver island. We observe strong plasmonic coupling between the spatially separated gold particles mediated by the connecting silver particle with almost no dissipation of energy. As the excitation energy of the silver island exceeds that of the gold particles, only quasi-occupation of the silver transfer channel is possible. We describe this effect both with exact classical electrodynamic modeling and qualitative quantum-mechanical calculations. We identify the formation of strong hot spots between all particles as the main mechanism for the loss-less coupling and thus coherent ultra-fast energy transfer between the remote partners. Our findings could prove useful for quantum gate operations, but also for classical charge and information transfer processes., Comment: 35 pages, 14 figures, includes SI

DNA self‐assembly is a powerful tool to arrange optically active components with high accuracy in a large parallel manner. A facile approach to assemble plasmonic antennas consisting of two metallic nanoparticles (40 nm) with a single colloidal quantum dot positioned at the hot spot is presented here. The design approach is based on DNA complementarity, stoichiometry, and steric hindrance principles. Since no intermediate molecules other than short DNA strands are required, the structures possess a very small gap (≈ 5 nm) which is desired to achieve high Purcell factors and plasmonic enhancement. As a proof‐of‐concept, the fluorescence emission from antennas assembled with both conventional and ultrasmooth spherical gold particles is measured. An increase in fluorescence is obtained, up to ≈30‐fold, compared to quantum dots without antenna.

The self-assembly of nanoscale elements into three-dimensional structures with precise shapes and sizes is important in fields such as nanophotonics, metamaterials and biotechnology. Short molecular linkers have previously been used to create assemblies of nanoparticles, but the approach is limited to small interparticle distances, typically less than 10 nm. Alternatively, DNA origami can precisely organize nanoscale objects over much larger length scales. Here we show that rigid DNA origami scaffolds can be used to assemble metal nanoparticles, quantum dots and organic dyes into hierarchical nanoclusters that have a planet-satellite-type structure. The nanoclusters have a tunable stoichiometry, defined distances of 5-200 nm between components, and controllable overall sizes of up to 500 nm. We also show that the nanoscale components can be positioned along the radial DNA spacers of the nanostructures, which allows short- and long-range interactions between nanoparticles and dyes to be studied in solution. The approach could, in the future, be used to construct efficient energy funnels, complex plasmonic architectures, and porous, nanoengineered scaffolds for catalysis.

We study the distance-dependent quenching of fluorescence due to a metallic nanoparticle in proximity of a fluorophore. In our single-molecule measurements, we achieve excellent control over structure and stoichiometry by using self-assembled DNA structures (DNA origami) as a breadboard where both the fluorophore and the 10 nm metallic nanoparticle are positioned with nanometer precision. The single-molecule spectroscopy method employed here reports on the co-localization of particle and dye, while fluorescence lifetime imaging is used to directly obtain the correlation of intensity and fluorescence lifetime for varying particle to dye distances. Our data can be well explained by exact calculations that include dipole dipole orientation and distances. Fitting with a more practical model for nanosurface energy transfer yields 10.4 nm as the characteristic distance of 50% energy transfer. The use of DNA nanotechnology together with minimal sample usage by attaching the particles to the DNA origami directly on the microscope coverslip paves the way for more complex experiments exploiting dye nanoparticle interactions. Fil: Acuna, Guillermo P.. Technische Universität Braunschweig; Alemania Fil: Bucher, Martina. Ludwig Maximilians Universitat; Alemania Fil: Stein, Ingo H.. Ludwig Maximilians Universitat; Alemania Fil: Steinhauer, Christian. Ludwig Maximilians Universitat; Alemania Fil: Kuzyk, Anton. Technische Universitat Munchen; Alemania Fil: Holzmeister, Phil. Technische Universität Braunschweig; Alemania Fil: Schreiber, Robert. Ludwig Maximilians Universitat; Alemania Fil: Moroz, Alexander. Fil: Stefani, Fernando Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; Argentina Fil: Liedl, Tim. Ludwig Maximilians Universitat; Alemania Fil: Simmel, Friedrich C.. Technische Universitat Munchen; Alemania Fil: Tinnefeld, Philip. Technische Universität Braunschweig; Alemania

The application of three-dimensional DNA origami objects as rigid mechanical mediators or force sensing elements requires detailed knowledge about their complex mechanical properties. Using magnetic tweezers, we directly measure the bending and torsional rigidities of four- and six-helix bundles assembled by this technique. Compared to duplex DNA, we find the bending rigidities to be greatly increased while the torsional rigidities are only moderately augmented. We present a mechanical model explicitly including the crossovers between the individual helices in the origami structure that reproduces the experimentally observed behavior. Our results provide an important basis for the future application of 3D DNA origami in nanomechanics.

Tensegrity or tensional integrity is a property of a structure that relies on a balance between components that are either in pure compression or in pure tension for its stability [1,2]. Tensegrity structures exhibit extremely high strength-to-weight ratios and great resilience, and are therefore widely used in engineering, robotics and architecture [3,4]. Here we report nanoscale, prestressed, three-dimensional tensegrity structures in which rigid bundles of DNA double helices resist compressive forces exerted by segments of single-stranded DNA that act as tension-bearing cables. Our DNA tensegrity structures can self-assemble against forces up to 14 pN, which is twice the stall force of powerful molecular motors such as kinesin or myosin [5,6]. The forces generated by this molecular prestressing mechanism can be employed to bend the DNA bundles or to actuate the entire structure through enzymatic cleavage at specific sites. In addition to being building blocks for nanostructures, tensile structural elements made of single-stranded DNA could be used to study molecular forces, cellular mechanotransduction, and other fundamental biological processes.

Self-assembled DNA nanostructures have been used to create man-made transmembrane channels in lipid bilayers. Here, we present a DNA-tile structure with a nominal subnanometer channel and cholesterol-tags for membrane anchoring. With an outer diameter of 5 nm and a molecular weight of 45 kDa, the dimensions of our synthetic nanostructure are comparable to biological ion channels. Because of its simple design, the structure self-assembles within a minute, making its creation scalable for applications in biology. Ionic current recordings demonstrate that the tile structures enable ion conduction through lipid bilayers and show gating and voltage-switching behavior. By demonstrating the design of DNA-based membrane channels with openings much smaller than that of the archetypical six-helix bundle, our work showcases their versatility inspired by the rich diversity of natural membrane components.

Biological membranes fulfill many important tasks within living organisms. In addition to separating cellular volumes, membranes confine the space available to membrane-associated proteins to two dimensions (2D), which greatly increases their probability to interact with each other and assemble into multiprotein complexes. We here employed two DNA origami structures functionalized with cholesterol moieties as membrane anchors--a three-layered rectangular block and a Y-shaped DNA structure--to mimic membrane-assisted assembly into hierarchical superstructures on supported lipid bilayers and small unilamellar vesicles. As designed, the DNA constructs adhered to the lipid bilayers mediated by the cholesterol anchors and diffused freely in 2D with diffusion coefficients depending on their size and number of cholesterol modifications. Different sets of multimerization oligonucleotides added to bilayer-bound origami block structures induced the growth of either linear polymers or two-dimensional lattices on the membrane. Y-shaped DNA origami structures associated into triskelion homotrimers and further assembled into weakly ordered arrays of hexagons and pentagons, which resembled the geometry of clathrin-coated pits. Our results demonstrate the potential to realize artificial self-assembling systems that mimic the hierarchical formation of polyhedral lattices on cytoplasmic membranes.

Circular dichroism spectra of naturally occurring molecules and also of synthetic chiral arrangements of plasmonic particles often exhibit characteristic bisignate shapes. Such spectra consist of peaks next to dips (or vice versa) and result from the superposition of signals originating from many individual chiral objects oriented randomly in solution. Here we show that by first aligning and then toggling the orientation of DNA-origami-scaffolded nanoparticle helices attached to a substrate, we are able to reversibly switch the optical response between two distinct circular dichroism spectra corresponding to either perpendicular or parallel helix orientation with respect to the light beam. The observed directional circular dichroism of our switchable plasmonic material is in good agreement with predictions based on dipole approximation theory. Such dynamic metamaterials introduce functionality into soft matter-based optical devices and may enable novel data storage schemes or signal modulators., Plasmonic resonances in nanoparticle helices arranged by the DNA origami method can give rise to strong circular dichroism at visible wavelengths. Schreiber et al. show that aligning and then toggling the orientation of such nanoparticle helices enables reversible switching of the dichroic response.

We report a method for simultaneous ionic current measurements of single molecules across up to 16 solid state nanopore channels. Each device, costing less than $20, contains 16 glass nanopores made by laser assisted capillary pulling. We demonstrate simultaneous multichannel detection of double stranded DNA and trapping of DNA origami nanostructures to form hybrid nanopores.

Nanopillars are promising nanostructures composed of various materials that bring new functionalities for applications ranging from photovoltaics to analytics. We developed DNA nanopillars with a height of 220 nm and a diameter of ~14 nm using the DNA origami technique. Modifying the base of the nanopillars with biotins allowed selective, upright, and rigid immobilization on solid substrates. With the help of site-selective dye labels, we visualized the structure and determined the orientation of the nanopillars by three-dimensional fluorescence superresolution microscopy. Because of their rigidity and nanometer-precise addressability, DNA origami nanopillars qualify as scaffold for the assembly of plasmonic devices as well as for three-dimensional superresolution standards.

Designing nanoscale objects with the potential to perform externally-controlled motion in biological environments is one of the most sought-after objectives in nanotechnology. Different types of chemically and physically-powered motors have been prepared at the macro- and microscale. However, the preparation of nanoscale objects with a complex morphology, and the potential for light-driven motion has remained elusive to date. Here, we go a step forward by designing a nanoscale hybrid with a propeller-resembling shape, which can be controlled by focused light under biological conditions. Our hybrid, hereafter ‘Au@DNA-origami’, consists of a spherical gold nanoparticle with self-assembled, biocompatible, two-dimensional (2D) DNA sheets on its surface. As a first step towards the potential utilization of these nanoscale objects as light-driven assemblies in biological environments, we show that they can be optically trapped, and hence translated and deposited on-demand, and that under realistic trapping conditions the thermally-induced dehybridization of the DNA sheets can be avoided.

Molecular self-assembly offers a ‘bottom-up’ route to fabrication with subnanometre precision of complex structures from simple components1. DNA has proven a versatile building block2–5 for programmable construction of such objects, including two-dimensional crystals6, nanotubes7–11, and three-dimensional wireframe nanopolyhedra12–17. Templated self-assembly of DNA18 into custom two-dimensional shapes on the megadalton scale has been demonstrated previously with a multiple-kilobase ‘scaffold strand’ that is folded into a flat array of antiparallel helices by interactions with hundreds of oligonucleotide ‘staple strands’19, 20. Here we extend this method to building custom three-dimensional shapes formed as pleated layers of helices constrained to a honeycomb lattice. We demonstrate the design and assembly of nanostructures approximating six shapes — monolith, square nut, railed bridge, genie bottle, stacked cross, slotted cross — with precisely controlled dimensions ranging from 10 to 100 nm. We also show hierarchical assembly of structures such as homomultimeric linear tracks and of heterotrimeric wireframe icosahedra. Proper assembly requires week-long folding times and calibrated monovalent and divalent cation concentrations. We anticipate that our strategy for self-assembling custom three-dimensional shapes will provide a general route to the manufacture of sophisticated devices bearing features on the nanometer scale.

We propose a method to detect and track multiple moving biological spot-like particles showing different kinds of dynamics in image sequences acquired through multidimensional fluorescence microscopy. It enables the extraction and analysis of information such as number, position, speed, movement, and diffusion phases of, e.g., endosomal particles. The method consists of several stages. After a detection stage performed by a three-dimensional (3-D) undecimated wavelet transform, we compute, for each detected spot, several predictions of its future state in the next frame. This is accomplished thanks to an interacting multiple model (IMM) algorithm which includes several models corresponding to different biologically realistic movement types. Tracks are constructed, thereafter, by a data association algorithm based on the maximization of the likelihood of each IMM. The last stage consists of updating the IMM filters in order to compute final estimations for the present image and to improve predictions for the next image. The performances of the method are validated on synthetic image data and used to characterize the 3-D movement of endocytic vesicles containing quantum dots.