Lateral Flow Assay Biotesting by Utilizing Plasmonic Nanoparticles Made of Inexpensive Metals─Replacing Colloidal Gold.

Nanoparticles (NPs) can be conjugated with diverse biomolecules and employed in biosensing to detect target analytes in biological samples. This proven concept was primarily used during the COVID-19 pandemic with gold-NP-based lateral flow assays (LFAs). Considering the gold price and its worldwide depletion, here we show that novel plasmonic NPs based on inexpensive metals, titanium nitride (TiN) and copper covered with a gold shell (Cu@Au), perform comparable to or even better than gold nanoparticles. After conjugation, these novel nanoparticles provided high figures of merit for LFA testing, such as high signals and specificity and robust naked-eye signal recognition. Since the main cost of Au NPs in commercial testing kits is the colloidal synthesis, our development with the Cu@Au and the laser-ablation-fabricated TiN NPs is exciting, offering potentially inexpensive plasmonic nanomaterials for various bioapplications. Moreover, our machine learning study showed that biodetection with TiN is more accurate than that with Au.

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.

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.

Environment-Dependent Stability and Mechanical Properties of DNA Origami Six-Helix Bundles with Different Crossover Spacings.

The internal design of DNA nanostructures defines how they behave in different environmental conditions, such as endonuclease-rich or low-Mg2+ solutions. Notably, the inter-helical crossovers that form the core of such DNA objects have a major impact on their mechanical properties and stability. Importantly, crossover design can be used to optimize DNA nanostructures for target applications, especially when developing them for biomedical environments. To elucidate this, two otherwise identical DNA origami designs are presented that have a different number of staple crossovers between neighboring helices, spaced at 42- and 21- basepair (bp) intervals, respectively. The behavior of these structures is then compared in various buffer conditions, as well as when they are exposed to enzymatic digestion by DNase I. The results show that an increased number of crossovers significantly improves the nuclease resistance of the DNA origami by making it less accessible to digestion enzymes but simultaneously lowers its stability under Mg2+ -free conditions by reducing the malleability of the structures. Therefore, these results represent an important step toward rational, application-specific DNA nanostructure design.

Probing the Conformational States of a pH-Sensitive DNA Origami Zipper via Label-Free Electrochemical Methods.

DNA origami structures represent an exciting class of materials for use in a wide range of biotechnological applications. This study reports the design, production, and characterization of a DNA origami "zipper" structure, which contains nine pH-responsive DNA locks. Each lock consists of two parts that are attached to the zipper's opposite arms: a DNA hairpin and a single-stranded DNA that are able to form a DNA triplex through Hoogsteen base pairing. The sequences of the locks were selected in a way that the zipper adopted a closed configuration at pH 6.5 and an open state at pH 8.0 (transition pKa 7.6). By adding thiol groups, it was possible to immobilize the zipper structure onto gold surfaces. The immobilization process was characterized electrochemically to confirm successful adsorption of the zipper. The open and closed states were then probed using differential pulse voltammetry and electrochemical impedance spectroscopy with solution-based redox agents. It was found that after immobilization, the open or closed state of the zipper in different pH regimes could be determined by electrochemical interrogation. These findings pave the way for development of DNA origami-based pH monitoring and other pH-responsive sensing and release strategies for zipper-functionalized gold surfaces.

Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems.

DNA nanotechnology provides an excellent foundation for diverse nanoscale structures that can be used in various bioapplications and materials research. Among all existing DNA assembly techniques, DNA origami proves to be the most robust one for creating custom nanoshapes. Since its invention in 2006, building from the bottom up using DNA advanced drastically, and therefore, more and more complex DNA-based systems became accessible. So far, the vast majority of the demonstrated DNA origami frameworks are static by nature; however, there also exist dynamic DNA origami devices that are increasingly coming into view. In this review, we discuss DNA origami nanostructures that exhibit controlled translational or rotational movement when triggered by predefined DNA sequences, various molecular interactions, and/or external stimuli such as light, pH, temperature, and electromagnetic fields. The rapid evolution of such dynamic DNA origami tools will undoubtedly have a significant impact on molecular-scale precision measurements, targeted drug delivery and diagnostics; however, they can also play a role in the development of optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.

Doxorubicin-loaded DNA origami nanostructures: stability in vitreous and their uptake and toxicity in ocular cells.

Biocompatibility and precise control over their size and shape make DNA origami nanostructures (DONs) promising for drug delivery applications. Whilst many investigations have focused on cancer treatment, this might not be the best fit for DONs that get degraded by nucleases in blood. In comparison, an eye is a uniquely isolated target organ, which could benefit from DONs to achieve and maintain therapeutic concentrations in diseases that threaten the eyesight of millions of patients every year. We investigated the loading of doxorubicin (DOX) as a model drug into three distinct DONs and tested their stability upon storage. Further, we chose one structure (24HB) to probe its stability under physiological conditions in cell media and porcine vitreous, before examining the uptake and effect of DOX-loaded 24HB (24HB-DOX) on the cell viability in a retinal cell line (ARPE-19). Similar to previous reports, the tested low µM loading concentrations of DOX resulted in high drug loadings of up to 34% (m/m), and remained mostly intact in water for at least 2 months at 4 °C. In cell media and porcine vitreous at 37 °C, however, 24HB required additional Mg2+ supplementation to avoid degradation and the loss of the attached fluorophores. With added Mg2+, 24HB remained stable in vitreous for 7 days at 37 °C. The treatment with 24HB-DOX was well tolerated by ARPE-19 cells, compared to the observed higher toxicity of free DOX. Uptake studies revealed, however, that in contrast to free DOX, very little 24HB-DOX was taken up by the cells. Instead, the particles were observed to attach around the cells. Hence, our results suggest that since the uptake seems to be the bottleneck for therapies using DONs, further strategies such as adding ocular targeting moieties are necessary to increase the uptake and efficacy of doxorubicin-loaded DONs.

Lateral Flow Assays Biotesting by Utilizing Plasmonic Nanoparticles Made of Inexpensive Metals - Replacing Colloidal Gold.

Nanoparticles (NPs) can be conjugated with diverse biomolecules and employed in biosensing to detect target analytes in biological samples. This proven concept was primarily used during the COVID-19 pandemic with gold NPs-based lateral flow assays (LFAs). Considering the gold price and its worldwide depletion, here we show that novel plasmonic nanoparticles (NPs) based on inexpensive metals, titanium nitride (TiN) and copper covered with a gold shell (Cu@Au), perform comparable or even better than gold nanoparticles. After conjugation, these novel nanoparticles provided high figures of merit for LFA testing, such as high signals and specificity and robust naked-eye signal recognition. To the best of our knowledge, our study represents the 1st application of laser-ablation-fabricated nanoparticles (TiN) in the LFA and dot-blot biotesting. Since the main cost of the Au NPs in commercial testing kits is in the colloidal synthesis, our development with TiN is very exciting, offering potentially very inexpensive plasmonic nanomaterials for various bio-testing applications. Moreover, our machine learning study showed that the bio-detection with TiN is more accurate than that with Au.

Protein Coating of DNA Origami.

DNA origami has emerged as a common technique to create custom two- (2D) and three-dimensional (3D) structures at the nanoscale. These DNA nanostructures have already proven useful in development of many biotechnological tools; however, there are still challenges that cast a shadow over the otherwise bright future of biomedical uses of these DNA objects. The rather obvious obstacles in harnessing DNA origami as drug-delivery vehicles and/or smart biodevices are related to their debatable stability in biologically relevant media, especially in physiological low-cation and endonuclease-rich conditions, relatively poor transfection rates, and, although biocompatible by nature, their unpredictable compatibility with the immune system. Here we demonstrate a technique for coating DNA origami with albumin proteins for enhancing their pharmacokinetic properties. To facilitate protective coating, a synthesized positively charged dendron was linked to bovine serum albumin (BSA) through a covalent maleimide-cysteine bonding, and then the purified dendron-protein conjugates were let to assemble on the negatively charged surface of DNA origami via electrostatic interaction. The resulted BSA-dendron conjugate-coated DNA origami showed improved transfection, high resistance against endonuclease digestion, and significantly enhanced immunocompatibility compared to bare DNA origami. Furthermore, our proposed coating strategy can be considered highly versatile as a maleimide-modified dendron serving as a synthetic DNA-binding domain can be linked to any protein with an available cysteine site.

Signal Amplification in Electrochemical DNA Biosensors Using Target-Capturing DNA Origami Tiles.

Electrochemical DNA (e-DNA) biosensors are feasible tools for disease monitoring, with their ability to translate hybridization events between a desired nucleic acid target and a functionalized transducer, into recordable electrical signals. Such an approach provides a powerful method of sample analysis, with a strong potential to generate a rapid time to result in response to low analyte concentrations. Here, we report a strategy for the amplification of electrochemical signals associated with DNA hybridization, by harnessing the programmability of the DNA origami method to construct a sandwich assay to boost charge transfer resistance (RCT) associated with target detection. This allowed for an improvement in the sensor limit of detection by two orders of magnitude compared to a conventional label-free e-DNA biosensor design and linearity for target concentrations between 10 pM and 1 nM without the requirement for probe labeling or enzymatic support. Additionally, this sensor design proved capable of achieving a high degree of strand selectivity in a challenging DNA-rich environment. This approach serves as a practical method for addressing strict sensitivity requirements necessary for a low-cost point-of-care device.

Optically Responsive Protein Coating of DNA Origami for Triggered Antigen Targeting.

DNA nanostructures have emerged as modular building blocks in several research fields including biomedicine and nanofabrication. Their proneness to degradation in various environments has led to the development of a variety of nature-inspired protection strategies. Coating of DNA origami nanostructures with proteins can circumvent degradation and alter their properties. Here, we have used a single-chain variable antibody fragment and serum albumin to construct positively charged and stimuli-responsive protein-dendron conjugates, which were complexed with DNA origami through electrostatic interactions. Using a stepwise assembly approach, the coated nanostructures were studied for their interaction with the corresponding antigen in fluorescence-based immunoassays. The results suggest that the antibody-antigen interaction can be disturbed by the addition of the bulky serum albumin. However, this effect is fully reversible upon irradiation of the structures with an optical stimulus. This leads to a selective dissociation of the serum albumin from the nanostructure due to cleavage of a photolabile group integrated in the dendron structure, exposing the antibody fragment and enabling triggered binding to the antigen, demonstrating that serum albumin can be considered as an externally controlled "camouflaging" agent. The presented stimuli-responsive complexation approach is highly versatile regarding the choice of protein components and could, therefore, find use in DNA origami protection, targeting, and delivery as well as their spatiotemporal control.

Prospective Cancer Therapies Using Stimuli-Responsive DNA Nanostructures.

Nanostructures based on DNA self-assembly present an innovative way to address the increasing need for target-specific delivery of therapeutic molecules. Currently, most of the chemotherapeutics being used in clinical practice have undesired and exceedingly high off-target toxicity. This is a challenge in particular for small molecules, and hence, developing robust and effective methods to lower these side effects and enhance the antitumor activity is of paramount importance. Prospectively, these issues could be tackled with the help of DNA nanotechnology, which provides a route for the fabrication of custom, biocompatible, and multimodal structures, which can, to some extent, resist nuclease degradation and survive in the cellular environment. Similar to widely employed liposomal products, the DNA nanostructures (DNs) are loaded with selected drugs, and then by employing a specific stimulus, the payload can be released at its target region. This review explores several strategies and triggers to achieve targeted delivery of DNs. Notably, different modalities are explained through which DNs can interact with their respective targets as well as how structural changes triggered by external stimuli can be used to achieve the display or release of the cargo. Furthermore, the prospects and challenges of this technology are highlighted.

Reconfigurable DNA Origami Nanocapsule for pH-Controlled Encapsulation and Display of Cargo.

DNA nanotechnology provides a toolbox for creating custom and precise nanostructures with nanometer-level accuracy. These nano-objects are often static by nature and serve as versatile templates for assembling various molecular components in a user-defined way. In addition to the static structures, the intrinsic programmability of DNA nanostructures allows the design of dynamic devices that can perform predefined tasks when triggered with external stimuli, such as drug delivery vehicles whose cargo display or release can be triggered with a specified physical or chemical cue in the biological environment. Here, we present a DNA origami nanocapsule that can be loaded with cargo and reversibly opened and closed by changing the pH of the surrounding solution. Moreover, the threshold pH value for opening/closing can be rationally designed. We characterize the reversible switching and a rapid opening of "pH-latch"-equipped nanocapsules using Förster resonance energy transfer. Furthermore, we demonstrate the full cycle of capsule loading, encapsulation, and displaying the payload using metal nanoparticles and functional enzymes as cargo mimics at physiologically relevant ion concentrations.

DNA Origami-Mediated Substrate Nanopatterning of Inorganic Structures for Sensing Applications.

Structural DNA nanotechnology provides a viable route for building from the bottom-up using DNA as construction material. The most common DNA nanofabrication technique is called DNA origami, and it allows high-throughput synthesis of accurate and highly versatile structures with nanometer-level precision. Here, it is shown how the spatial information of DNA origami can be transferred to metallic nanostructures by combining the bottom-up DNA origami with the conventionally used top-down lithography approaches. This allows fabrication of billions of tiny nanostructures in one step onto selected substrates. The method is demonstrated using bowtie DNA origami to create metallic bowtie-shaped antenna structures on silicon nitride or sapphire substrates. The method relies on the selective growth of a silicon oxide layer on top of the origami deposition substrate, thus resulting in a patterning mask for following lithographic steps. These nanostructure-equipped surfaces can be further used as molecular sensors (e.g., surface-enhanced Raman spectroscopy (SERS)) and in various other optical applications at the visible wavelength range owing to the small feature sizes (sub-10 nm). The technique can be extended to other materials through methodological modifications; therefore, the resulting optically active surfaces may find use in development of metamaterials and metasurfaces.

Structural stability of DNA origami nanostructures under application-specific conditions.

With the introduction of the DNA origami technique, it became possible to rapidly synthesize almost arbitrarily shaped molecular nanostructures at nearly stoichiometric yields. The technique furthermore provides absolute addressability in the sub-nm range, rendering DNA origami nanostructures highly attractive substrates for the controlled arrangement of functional species such as proteins, dyes, and nanoparticles. Consequently, DNAorigami nanostructures have found applications in numerous areas of fundamental and applied research, ranging from drug delivery to biosensing to plasmonics to inorganic materials synthesis. Since many of those applications rely on structurally intact, well-definedDNA origami shapes, the issue of DNA origami stability under numerous application-relevant environmental conditions has received increasing interest in the past few years. In this mini-review we discuss the structural stability, denaturation, and degradation of DNA origami nanostructures under different conditions relevant to the fields of biophysics and biochemistry, biomedicine, and materials science, and the methods to improve their stability for desired applications.