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Chirality is a fundamental feature in all domains of nature, ranging from particle physics over electromagnetism to chemistry and biology. Chiral objects lack a mirror plane and inversion symmetry and therefore cannot be spatially aligned with their mirrored counterpart, their enantiomer. Both natural molecules and artificial chiral nanostructures can be characterized by their light-matter interaction, which is reflected in circular dichroism (CD). Using DNA origami, we assemble model meta-molecules from multiple plasmonic nanoparticles, representing meta-atoms accurately positioned in space. This allows us to reconstruct piece by piece the impact of varying macromolecular geometries on their surrounding optical near fields. Next to the emergence of CD signatures in the instance that we architect a third dimension, we design and implement sign-flipping signals through addition or removal of single particles in the artificial molecules. Our data and theoretical modeling reveal the hitherto unrecognized phenomenon of chiral plasmonic-dielectric coupling, explaining the intricate electromagnetic interactions within hybrid DNA-based plasmonic nanostructures.

Nanoscale stepper motors such as kinesin and dynein play a key role in numerous natural processes such as mitotic spindle formation during cell division or intracellular organelle transport. Their high efficacy in terms of operational speed and processivity has inspired the investigation of biomimetic technologies based on the use of programmable molecules. In particular, several designs of molecular walkers have been explored using DNA nanotechnology. Here, we study the actuation of a DNA-origami walker on a DNA-origami track based on three principles: 1) octapedal instead of bipedal walking for greater redundancy; 2) three pairs of orthogonal sequences, each of which fuels one repeatable stepping phase for cyclically driven motion with controlled directionality based on strain-based step selection; 3) designed size of only 3.5 nm per step on an origami track. All three principles are innovative in the sense that earlier demonstrations of steppers relied on a maximum of four legs on at least four orthogonal sequences to drive cyclic stepping, and took steps much larger than 3.4 nm in size. Using gel electrophoresis and negative-stain electron microscopy, we demonstrate cyclic actuation of DNA-origami structures through states defined by three sets of specific sequences of anchor points. However, this mechanism was not able to provide the intended control over directionality of movement. DNA-origami-based stepper motors will offer a future platform for investigating how increasing numbers of legs can be exploited to achieve robust stepping with relatively small step sizes.

In viscous fluids, motile microentities such as bacteria or artificial swimmers often display different transport modes than macroscopic ones. A current challenge in the field aims at using friction asymmetry to steer the motion of microscopic particles. Here we show that lithographically shaped magnetic microtriangles undergo a series of complex transport modes when driven by a precessing magnetic field, including a surfing-like drift close to the bottom plane. In this regime, we exploit the triangle asymmetric shape to obtain a transversal drift which is later used to transport the microtriangle in any direction along the plane. We explain this friction-induced anisotropic sliding with a minimal numerical model capable to reproduce the experimental results. Due to the flexibility offered by soft-lithographic sculpturing, our method to guide anisotropic-shaped magnetic microcomposites can be potentially extended to many other field responsive structures operating in fluid media.

Plasmonic nanoparticles have unique properties which can be harnessed to manipulate light at the nanoscale. With recent advances in synthesis protocols that increase their stability, gold-silver core-shell nanoparticles have become suitable building blocks for plasmonic nanostructures to expand the range of attainable optical properties. Here we tune the plasmonic response of gold-silver core-shell nanorods over the visible spectrum by varying the thickness of the silver shell. Through the chiral arrangement of the nanorods with the help of various DNA origami designs, the spectral tunability of the plasmon resonance frequencies is transferred into circular dichroism signals covering the spectrum from 400 nm to 700 nm. Our approach could aid in the construction of better sensors as well as metamaterials with a tunable optical response in the visible region.

Assembling hybrid substrates with nanometer-scale precision and molecular addressability enables advances in such distant fields as material research and biosensing. As such, the combination of lithographic methods with 2D DNA origami self-assembly [1–4] has led, among others, to the development of photonic crystal cavity arrays [2] and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micron scale [5–7]. Here we extend this concept to the third dimension through mounting 3D DNA origami onto nano-patterned substrates followed by silicification [8, 9] to provide mechanical and chemical stability. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to 3D-position any inorganic and organic components that are compatible with DNA architectures [10–13]. This way, complex and 3D-patterend surfaces designed on the molecular level while reaching macroscopic dimensions could supersede energy-intensive manufacturing steps in substrate processing.

Atomic force microscopy (AFM) is a powerful technique for imaging molecules, macromolecular complexes, and nanoparticles with nanometer-resolution. However, AFM images are distorted by the shape of the tip used. These distortions can be corrected if the tip shape can be determined by scanning a sample with features sharper than the tip and higher than the object of interest. Here we present a 3D DNA origami structure as fiducial for tip reconstruction and image correction. Our fiducial is stable under a broad range of conditions and has sharp steps at different heights that enable reliable tip reconstruction from as few as ten fiducials. The DNA origami is readily co-deposited with biological and non-biological samples, achieves higher precision for the tip apex than polycrystalline samples, and dramatically improves the accuracy of the lateral dimensions determined from the images. Our fiducial thus enables accurate and precise AFM imaging for a broad range of applications.

Chiral plasmonic nanostructures exhibit anomalously strong chiroptical signals and offer the possibility to realize asymmetric photophysical and photochemical processes controlled by circularly polarized light. Here, we use a chiral DNA-assembled nanorod pair as a model system for chiral plasmonic photomelting. We show that both the enantiomeric excess and consequent circular dichroism can be controlled with chiral light. The nonlinear chiroptical response of our plasmonic system results from the chiral photothermal effect leading to selective melting of the DNA linker strands. Our study describes both the single-complex and collective heating regimes, which should be treated with different models. The chiral asymmetry factors of the calculated photothermal and photomelting effects exceed the values typical for the chiral molecular photochemistry at least 10-fold. Our proposed mechanism can be used to develop chiral photoresponsive systems controllable with circularly polarized light.

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...

Improving the stability of DNA origami structures with respect to thermal, chemical, and mechanical demands will be essential to fully explore the real-life applicability of DNA nanotechnology. Here we present a strategy to increase the mechanical resilience of individual DNA origami objects and 3D DNA origami crystals in solution as well as in the dry state. By encapsulating DNA origami in a protective silica shell using sol-gel chemistry, all the objects maintain their structural integrity. This allowed for a detailed structural analysis of the crystals in a dry state, thereby revealing their true 3D shape without lattice deformation and drying-induced collapse. Analysis by energy-dispersive X-ray spectroscopy showed a uniform silica coating whose thickness could be controlled through the precursor concentrations and reaction time. This strategy thus facilitates shape-controlled bottom-up synthesis of designable biomimetic silica structures through transcription from DNA origami.

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.

Biomolecules can undergo liquid–liquid phase separation (LLPS), forming dense droplets that are increasingly understood to be important for cellular function. Analogous systems are studied as early-life compartmentalization mechanisms, for applications as protocells, or as drug-delivery vehicles. In many of these situations, interactions between the droplet and enzymatic solutes are important to achieve certain functions. To explore this, we carried out experiments in which a model LLPS system, formed from DNA “nanostar” particles, interacted with a DNA-cleaving restriction enzyme, SmaI, whose activity degraded the droplets, causing them to shrink with time. By controlling adhesion of the DNA droplet to a glass surface, we were able to carry out time-resolved imaging of this “active dissolution” process. We found that the scaling properties of droplet shrinking were sensitive to the proximity to the dissolution (“boiling”) temperature of the dense liquid: For systems far from the boiling point, enzymes acted only on the droplet surface, while systems poised near the boiling point permitted enzyme penetration. This was corroborated by the observation of enzyme-induced vacuole-formation (“bubbling”) events, which can only occur through enzyme internalization, and which occurred only in systems poised near the boiling point. Overall, our results demonstrate a mechanism through which the phase stability of a liquid affects its enzymatic degradation through modulation of enzyme transport properties.

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.

Doxorubicin (DOX) is a commonly employed drug in cancer chemotherapy, and its high DNA-binding affinity can be harnessed in preparing programmable DOX-loaded DNA nanostructures that can be further tailored for targeted delivery and therapeutics. Although DOX has been widely studied, the existing literature of promising DOX-loaded DNA nanocarriers remains limited and incoherent. A number of reports have over-looked the fundamentals of the DOX-DNA interaction, let alone the peculiarities arising from the complexity of the system as a whole. Here, based on an in-depth spectroscopic analysis, we characterize and optimize the DOX loading into different 2D and 3D scaffolded DNA origami nanostructures. In our experimental conditions, all of our DNA origami designs show rather similar DOX binding capacities, which are, however, remarkably lower than previously reported. To simulate the possible physiological degradation pathways, we examine the stability and DOX release properties of the complexes upon DNase I digestion, which reveals that they disintegrate and release DOX into the surroundings at characteristic rates related to the DNA origami superstructure and the loaded DOX content. In addition, we identify DOX self-aggregation and precipitation mechanisms and spectral changes linked to pH, magnesium, and DOX concentration that have been largely ignored in experimenting with DNA nanostructures and in spectroscopic analysis performed with routine UV-Vis and fluorescence techniques. Nevertheless, we demonstrate the possibility of customizing drug release profiles through rational DNA origami design. Therefore, we believe this work can be used as a guide to tailor the release profiles and develop better drug delivery systems based on DNA nanostructures.

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.

DNA double-strand breaks (DSBs) pose an everyday threat to the conservation of genetic information and therefore life itself. Several pathways have evolved to repair these cytotoxic lesions by rejoining broken ends, among them the nonhomologous end-joining mechanism that utilizes a DNA ligase. Here, we use a custom-designed DNA origami nanostructure as a model system to specifically mimic a DNA DSB, enabling us to study the end-joining of two fluorescently labeled DNA with the T4 DNA ligase on the single-molecule level. The ligation reaction is monitored by Forster resonance energy transfer (FRET) experiments both in solution and on surface-anchored origamis. Due to the modularity of DNA nanotechnology, DNA double strands with different complementary overhang lengths can be studied using the same DNA origami design. We show that the T4 DNA ligase repairs sticky ends more efficiently than blunt ends and that the ligation efficiency is influenced by both DNA sequence and the incubation conditions. Before ligation, dynamic fluctuations of the FRET signal are observed due to transient binding of the sticky overhangs. After ligation, the FRET signal becomes static. Thus, we can directly monitor the ligation reaction through the transition from dynamic to static FRET signals. Finally, we revert the ligation process using a restriction enzyme digestion and religate the resulting blunt ends. The here-presented DNA origami platform is thus suited to study complex multistep reactions occurring over several cycles of enzymatic treatment.

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.

The TATA-binding protein (TBP) and a transcription factor (TF) IIB-like factor compound the fundamental core of all eukaryotic initiation complexes. The reason for the emergence and strict requirement of the additional intiation factor Bdp1, which is unique to the RNA polymerase (RNAP) III sytem, however, remained elusive. A poorly studied aspect in this context is the effect of DNA strain, that arises from DNA compaction and transcriptional activity, on the efficiency of initiation complex formation. We made use of a new nanotechnological tool – a DNA origami-based force clamp - to follow the assembly of human initiation complexes in the Pol II and Pol III system at the single-molecule level under piconewton forces. We demonstrate that TBP-DNA complexes are force-sensitive and TFIIB is necessary and sufficient to stabilise TBP on a strained RNAP II promoter. In contrast, Bdp1 is the pivotal component that ensures stable anchoring of initiation factors, and thus the polymerase itself, in the RNAP III system. Thereby, we offer an explanation for the crucial role of Bdp1 for the high transcriptional output of Pol III genes for the first time.

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 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.

In biological systems, order typically emerges from out-of-equilibrium molecular processes that control both static patterns and dynamic changes. Now, the self-regulating assembly and disassembly of a synthetic system has been achieved on the micrometre scale, by coupling the growth of a DNA nanotube to a biochemical oscillator.

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.

The application of commonly used force spectroscopy in biological systems is often limited by the need for an invasive tether connecting the molecules of interest to a bead or cantilever tip. Here we present a DNA origami‐based prototype in a comparative binding assay. It has the advantage of in situ readout without any physical connection to the macroscopic world. The seesaw‐like structure has a lever that is able to move freely relative to its base. Binding partners on each side force the structure into discrete and distinguishable conformations. Model experiments with competing DNA hybridisation reactions yielded a drastic shift towards the conformation with the stronger binding interaction. With reference DNA duplexes of tuneable length on one side, this device can be used to measure ligand interactions in comparative assays.

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.