Controlling the size and adhesion of DNA droplets using surface- enriched DNA molecules.

Liquid droplets of biomolecules serve as organizers of the cellular interior and are of interest in biosensing and biomaterials applications. Here, we investigate means to tune the interfacial properties of a model biomolecular liquid consisting of multi-armed DNA 'nanostar' particles. We find that long DNA molecules that have binding affinity for the nanostars are preferentially enriched on the interface of nanostar droplets, thus acting as surfactants. Fluorescent measurements indicate that, in certain conditions, the interfacial density of the surfactant is around 20 per square micron, indicative of a sparse brush-like structure of the long, polymeric DNA. Increasing surfactant concentration leads to decreased droplet size, down to the sub-micron scale, consistent with droplet coalesence being impeded by the disjoining pressure created by the brush-like surfactant layer. Added DNA surfactant also keeps droplets from adhering to both hydrophobic and hydrophilic solid surfaces, apparently due to this same disjoining effect of the surfactant layer. We thus demonstrate control of the size and adhesive properties of droplets of a biomolecular liquid, with implications for basic biophysical understanding of such droplets, as well as for their applied use.

DNA Origami Fiducial for Accurate 3D Atomic Force Microscopy Imaging.

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 codeposited with biological and nonbiological 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.

Unraveling the Chirality Transfer from Circularly Polarized Light to Single Plasmonic Nanoparticles.

Due to their broken symmetry, chiral plasmonic nanostructures have unique optical properties and numerous applications. However, there is still a lack of comprehension regarding how chirality transfer occurs between circularly polarized light (CPL) and these structures. Here, we thoroughly investigate the plasmon-assisted growth of chiral nanoparticles from achiral Au nanocubes (AuNCs) via CPL without the involvement of any chiral molecule stimulators. We identify the structural chirality of our synthesized chiral plasmonic nanostructures using circular differential scattering (CDS) spectroscopy, which is correlated with scanning electron microscopy imaging at both the single-particle and ensemble levels. Theoretical simulations, including hot-electron surface maps, reveal that the plasmon-induced chirality transfer is mediated by the asymmetric distribution of hot electrons on achiral AuNCs under CPL excitation. Furthermore, we shed light on how this plasmon-induced chirality transfer can also be utilized for chiral growth in bimetallic systems, such as Ag or Pd on AuNCs. The results presented here uncover fundamental aspects of chiral light-matter interaction and have implications for the future design and optimization of chiral sensors and chiral catalysis, among others.

Platinum-DNA Origami Hybrid Structures in Concentrated Hydrogen Peroxide.

The DNA origami technique allows fast and large-scale production of DNA nanostructures that stand out with an accurate addressability of their anchor points. This enables the precise organization of guest molecules on the surfaces and results in diverse functionalities. However, the compatibility of DNA origami structures with catalytically active matter, a promising pathway to realize autonomous DNA machines, has so far been tested only in the context of bio-enzymatic activity, but not in chemically harsh reaction conditions. The latter are often required for catalytic processes involving high-energy fuels. Here, we provide proof-of-concept data showing that DNA origami structures are stable in 5 % hydrogen peroxide solutions over the course of at least three days. We report a protocol to couple these to platinum nanoparticles and show catalytic activity of the hybrid structures. We suggest that the presented hybrid structures are suitable to realize catalytic nanomachines combined with precisely engineered DNA nanostructures.

Unraveling the interaction between doxorubicin and DNA origami nanostructures for customizable chemotherapeutic drug release.

Doxorubicin (DOX) is a common drug in cancer chemotherapy, and its high DNA-binding affinity can be harnessed in preparing DOX-loaded DNA nanostructures for targeted delivery and therapeutics. Although DOX has been widely studied, the existing literature of DOX-loaded DNA-carriers remains limited and incoherent. Here, based on an in-depth spectroscopic analysis, we characterize and optimize the DOX loading into different 2D and 3D scaffolded DNA origami nanostructures (DONs). In our experimental conditions, all DONs show similar DOX binding capacities (one DOX molecule per two to three base pairs), and the binding equilibrium is reached within seconds, remarkably faster than previously acknowledged. To characterize drug release profiles, DON degradation and DOX release from the complexes upon DNase I digestion was studied. For the employed DONs, the relative doses (DOX molecules released per unit time) may vary by two orders of magnitude depending on the DON superstructure. In addition, we identify DOX aggregation mechanisms and spectral changes linked to pH, magnesium, and DOX concentration. These features have been largely ignored in experimenting with DNA nanostructures, but are probably the major sources of the incoherence of the experimental results so far. Therefore, we believe this work can act as a guide to tailoring the release profiles and developing better drug delivery systems based on DNA-carriers.

Enzymatic degradation of liquid droplets of DNA is modulated near the phase boundary.

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.

Friction Induces Anisotropic Propulsion in Sliding Magnetic Microtriangles.

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.

A label-free light-scattering method to resolve assembly and disassembly of DNA nanostructures.

DNA self-assembly, and in particular DNA origami, has evolved into a reliable workhorse for organizing organic and inorganic materials with nanometer precision and with exactly controlled stoichiometry. To ensure the intended performance of a given DNA structure, it is beneficial to determine its folding temperature, which in turn yields the best possible assembly of all DNA strands. Here, we show that temperature-controlled sample holders and standard fluorescence spectrometers or dynamic light-scattering setups in a static light-scattering configuration allow for monitoring the assembly progress in real time. With this robust label-free technique, we determine the folding and melting temperatures of a set of different DNA origami structures without the need for more tedious protocols. In addition, we use the method to follow digestion of DNA structures in the presence of DNase I and find strikingly different resistances toward enzymatic degradation depending on the structural design of the DNA object.

Three-phase DNA-origami stepper mechanism based on multi-leg interactions.

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.

Chiral Photomelting of DNA-Nanocrystal Assemblies Utilizing Plasmonic Photoheating.

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.

Nanoscale FasL Organization on DNA Origami to Decipher Apoptosis Signal Activation in Cells.

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 100× 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.

The Art of Designing DNA Nanostructures with CAD Software.

Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source.

A DNA Origami Platform for Single-Pair Förster Resonance Energy Transfer Investigation of DNA-DNA Interactions and Ligation.

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 Förster 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.

Cryopreservation of DNA Origami Nanostructures.

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.

DNA-Assembled Advanced Plasmonic Architectures.

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.

Chiral Plasmonic Nanocrystals for Generation of Hot Electrons: Toward Polarization-Sensitive Photochemistry.

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.

Directing Single-Molecule Emission with DNA Origami-Assembled Optical Antennas.

We demonstrate the capability of DNA self-assembled optical antennas to direct the emission of an individual fluorophore, which is free to rotate. DNA origami is used to fabricate optical antennas composed of two colloidal gold nanoparticles separated by a predefined gap and to place a single Cy5 fluorophore near the gap center. Although the fluorophore is able to rotate, its excitation and far-field emission is mediated by the antenna, with the emission directionality following a dipolar pattern according to the antenna main resonant mode. This work is intended to set out the basis for manipulating the emission pattern of single molecules with self-assembled optical antennas based on colloidal nanoparticles.

DNA-Mediated Self-Assembly of Plasmonic Antennas with a Single Quantum Dot in the Hot Spot.

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.

Position Accuracy of Gold Nanoparticles on DNA Origami Structures Studied with Small-Angle X-ray Scattering.

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.

DNA-Origami-Templated Silica Growth by Sol-Gel Chemistry.

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.