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Metallic nanoparticle dimers have been used to enhance the excitation rate of single‐quantum emitters. The interparticle distance (d) of the dimers has a crucial influence on the signal enhancement. Therefore, precise control of d is desired for optimal performance. However, statistical analysis of d has been often restricted to a small number of dimers due to the lack of reliable automatic software tools.For this reason, we developed a novel analysis tool for automatic dimer analysis. Our approach combines particle detection by circle Hough transformation (CHT) with custom classification routines optimised for distinct types of particles. We applied our tool to scanning electron microscopy (SEM) images and achieved great agreement in dimer detection, reaching an agreement of around 97% between automatic analysis and manual inspection for more than 3000 metallic nanoparticle dimers on DNA origami controlled by a combination of multiple DNA strands.Our study revealed the effects of the strand length (L) on the distribution of d. Based on geometric consideration, we expected a strong correlation between L and the standard deviation (σ) of d. We could verify this correlation by characterising four dimer designs with different L while analysing more than 1000 dimers per specimen. [ABSTRACT FROM AUTHOR]

Mosaic nanoparticle vaccines with heterotypic antigens exhibit broad‐spectrum antiviral capabilities, but the impact of antigen proportions and distribution patterns on vaccine‐induced immunity remains largely unexplored. Here, we present a DNA nanotechnology‐based strategy for spatially assembling heterotypic antigens to guide the rational design of mosaic nanoparticle vaccines. By utilizing two aptamers with orthogonal selectivity for the original SARS‐CoV‐2 spike trimer and Omicron receptor‐binding domain (RBD), along with a DNA soccer‐ball framework, we precisely manipulate the spacing, stoichiometry, and overall distribution of heterotypic antigens to create mosaic nanoparticles with average, bipolar, and unipolar antigen distributions. Systematic in vitro and in vivo immunological investigations demonstrate that 30 heterotypic antigens in equivalent proportions, with an average distribution, lead to higher production of broad‐spectrum neutralizing antibodies compared to the bipolar and unipolar distributions. Furthermore, the precise assembly utilizing our developed methodology reveals that a mere increment of five Omicron RBD antigens on a nanoparticle (from 15 to 20) not only diminishes neutralization against the Omicron variant but also triggers excessive inflammation. This work provides a unique perspective on the rational design of mosaic vaccines by highlighting the significance of the spatial placement and proportion of heterotypic antigens in their structure–activity mechanisms. [ABSTRACT FROM AUTHOR]

Self-assembling DNA nanoparticles have the potential to significantly advance the targeted delivery of molecular cargo owing to their chemical and architectural flexibility. Recently, it has been demonstrated that the genetic code embedded in DNA nanoparticles produced by the method of DNA origami or related techniques can be recognized and copied by RNA polymerase in vitro. Further, sculpted DNA nanoparticles can serve as a substrate for Cas9-mediated gene modification and gene expression in cell culture. In the present study, we further investigate the ability of DNA origami nanoparticles to be expressed in a human cell line with emphasis on the impact of single-stranded DNA (ssDNA) domains and the contributions of the architectural disposition of genetic control elements, namely promoter and enhancer sequences. Our findings suggest that while cells possess the remarkable capability to express genes within highly folded architectures, the presence and relative density and location of ssDNA domains appears to influence overall levels of gene expression. These results suggest that it may be possible to nuance folded DNA nanoparticle architecture to regulate the rate and/or level of gene expression. Considering the highly malleable architecture and chemistry of self-assembling DNA nanoparticles, these findings motivate further exploration of their potential as an economic nanotechnology platform for targeted gene editing, nucleic acid-based vaccines, and related biotherapeutic applications. [ABSTRACT FROM AUTHOR]

DNA origami nanostructures are promising carries for drug delivery applications. However, their limited stability under relevant conditions often presents a challenge. Herein, the structural stability of DNA origami nanostructures is investigated in a setting compatible with their application in photodynamic therapy (PDT). To this end, DNA origami triangles and six‐helix bundles (6HBs) are loaded with the clinically tested photosensitizer methylene blue, which upon irradiation with red light generates reactive oxygen species (ROS) that attack the DNA origami nanostructures. ROS‐induced structural damage is observed to depend on the ionic composition of the surrounding medium and becomes more severe at low ionic strength. Mg2+ ions can efficiently protect the DNA origami nanostructures from ROS‐induced damage and may even heal some of the damage obtained under Mg2+‐free conditions when added after irradiation. Finally, the employed DNA origami 6HBs are more resistant toward ROS‐induced structural damage than the triangles, which is attributed to their markedly different mechanical properties. These results thus provide some fundamental insights into the stabilizing role of DNA origami superstructure that may guide the selection or design of DNA origami nanocarriers with optimized stability for their application in PDT. [ABSTRACT FROM AUTHOR]

Chronic wound management is affected by three primary challenges: bacterial infection, oxidative stress and inflammation, and impaired regenerative capacity. Conventional treatment methods typically fail to deliver optimal outcomes, thus highlighting the urgency to develop innovative materials that can address these issues and improve efficacy. Recent advances in DNA nanotechnology have garnered significant interest, particularly in the field of functional nucleic acid (FNA) nanomaterials, owing to their exceptional biocompatibility, programmability, and therapeutic potential. Among them, FNAs with unique nanostructures have garnered considerable attention. First, they inherit the biological properties of FNAs, including biocompatibility, reactive oxygen species (ROS)-scavenging capabilities, and modulation of cellular functions. Second, based on a precise design, these nanostructures exhibit superior physical properties, stability, and cellular uptake. Third, by leveraging the programmability of DNA strands, FNA nanostructures can be customized to accommodate therapeutic nucleic acids, peptides, and small-molecule drugs, thereby enabling a stable and controlled drug delivery system. These unique characteristics enable the use of FNA nanostructures to effectively address the major challenges in chronic wound management. This review focuses on various FNA nanostructures, including tetrahedral framework nucleic acids (tFNAs), DNA hydrogels, DNA origami, and rolling-circle amplification (RCA) DNA assembly. Additionally, a summary of recent advancements in their design and application for chronic wound management as well as insights for future research in this field are provided. [Display omitted] [ABSTRACT FROM AUTHOR]

Plasmonic nanostructures are frequently utilized to create metasurfaces with a large variety of optical effects. Control over shape and positioning of the nanostructures is key to the function of such plasmonic metasurfaces. Next to lithographic means, directed self‐assembly is a viable route to create plasmonic structures on surfaces with the necessary precision. Here, a combined approach of DNA origami self‐assembly and electron beam lithography is presented for determinate positioning of gold nanospheres on a SiO2 surface. First, DNA origami structures bind to the electron beam‐patterned substrate and subsequently, gold nanoparticles attach to a defined binding site on the DNA origami structure via DNA hybridization. A sol‐gel reaction is then used to grow a silica layer around the DNA, thereby increasing the stability of the self‐assembled metasurface. A mean yield of 74% of single gold nanospheres is achieved located at the determinate positions with a spatial position accuracy of 9 nm. Gold nanosphere dimers and trimers are achieved with a rate of 65% and 60%, respectively. The applicability of this structuring method is demonstrated by the fabrication of metasurfaces whose optical response can be tuned by the polarization of the incoming and the scattered light. [ABSTRACT FROM AUTHOR]

Origami, the art of paper folding, has long fascinated researchers and designers in its potential to replicate and tap the complexity of nature. In this paper, we pursue the crossing of origami engineering structures and biology, the realm of biologically-inspired origami structures categorized by the two biggest taxonomy kingdoms and DNA origami. Given the diversity of life forms that Earth comprises, we pursue an analysis of biomimetic designs that resemble intricate patterns and functionalities occurring in nature. Our research begins by setting out a taxonomic framework for the classification of origami structures based on biologically important kingdoms. From each of these, we explore the engineering structures inspired by morphological features, behaviors, and ecological adaptations of organisms. We also discuss implications in realms such as sustainability, biomaterials development, and bioinspired robotics. Thus, by parlaying the principles found in nature's design playbook through the art of folding, biologically inspired origami becomes fertile ground for interdisciplinary collaboration and creativity. Through this approach, we aim to inspire readers, researchers, and designers to embark on a journey of discovery in which the boundaries between art, science, and nature are blurred, providing a foundation for innovation to thrive. [ABSTRACT FROM AUTHOR]

Atomic Force Microscopy (AFM), High‐Speed AFM (HS‐AFM) simulation AFM, and Localization AFM (LAFM) enable the study of molecules and surfaces with increasingly higher spatiotemporal resolution. However, effective and rapid analysis of the images and movies produced by these techniques can be challenging, often requiring the use of multiple image processing software applications and scripts. Here, NanoLocz, an open‐source solution that offers advanced analysis capabilities for the AFM community, is presented. Integration and continued development of AFM analysis tools is essential to improve access to data, increase throughput, and open new analysis opportunities. NanoLocz efficiently leverages the rich data AFM has to offer by incorporating and combining existing and newly developed analysis methods for AFM, HS‐AFM, simulation AFM, and LAFM seamlessly. It facilitates and streamlines AFM analysis workflows from import of raw data, through to various analysis workflows. Here, the study demonstrates the capabilities of NanoLocz and the new methods it enables including single‐molecule LAFM, time‐resolved LAFM, and simulation LAFM. [ABSTRACT FROM AUTHOR]

Inflammatory bowel disease (IBD) encompasses a collection of chronic inflammatory conditions impacting the gastrointestinal tract, with a discernible global rise in prevalence and severity. The overabundance of reactive oxygen species (ROS) in the intestinal environment leads disruption of local redox homeostasis, and perturbation of the gut microbiota, exacerbating IBD. Consequently, mitigating excess ROS and preserving gut microbiota homeostasis have emerged as effective approaches for IBD management. In this study, a triangular DNA origami nanostructure loaded with siRNA targeting tumor necrosis factor α (siTNF‐αtDON) is introduced for this purpose. This nanostructure demonstrates efficacy in eliminating ROS within cells closely associated with IBD, diminishing inflammation, and ameliorating disorders in gut microbiota, as evidenced in an IBD mouse model. Furthermore, this investigation demonstrates the effects of siTNF‐αtDON on related inflammatory signaling pathways, including NF‐κB, MAPK/ERK and Keap1/Nrf2. Collectively, this study offers insights into the potential utilization of DNA nanostructures as antioxidants and gut microbiota modulators, presenting promising avenues for the IBD treatment. [ABSTRACT FROM AUTHOR]

Interacting with living systems typically involves the ability to address lipid membranes of cellular systems. The first step of interaction of a nanorobot with a cell will thus be the detection of binding to a lipid membrane. Utilizing DNA origami, we engineered a biosensor with single‐molecule Fluorescence Resonance Energy Transfer (smFRET) as transduction mechanism for precise lipid vesicle detection and cargo delivery. The system hinges on a hydrophobic ATTO647N modified single‐stranded DNA (ssDNA) leash, protruding from a DNA origami nanostructure. In a vesicle‐free environment, the ssDNA coils, ensuring high FRET efficiency. Upon vesicle binding to cholesterol anchors on the DNA origami, hydrophobic ATTO647N induces the ssDNA to stretch towards the lipid bilayer, reducing FRET efficiency. As the next step, the sensing strand serves as molecular cargo that can be transferred to the vesicle through a triggered strand displacement reaction. Depending on the number of cholesterols on the displacer strands, we either induce a diffusive release of the fluorescent load towards neighboring vesicles or a stoichiometric release of a single cargo‐unit to the vesicle on the nanosensor. Ultimately, our multi‐functional liposome interaction and detection platform opens up pathways for innovative biosensing applications and stoichiometric loading of vesicles with single‐molecule control. [ABSTRACT FROM AUTHOR]

Energy dissipation through physical downscaling towards more complex types of memory and logic devices, loss of ultrapure water and consumption of large amounts of (toxic) chemicals for wafer cleaning processes, as well as high thermal budget of solid-state synthesis and thin film growth of standard semiconductors including the use of rare earth elements – all this poses great challenges for semiconductor materials science and technology. Therefore, research and development of alternative methods for micro- and nanofabrication and chemical functionalization of a new type of resource- and energy-efficient semiconductors as the core component of every computer chip is crucial. One of the promising opportunities is the transformation of today's complementary metal-oxide-semiconductor (CMOS) electronics into ecofriendly and neuroinspired electronics driven by molecular design and multi-level switching mechanisms at room temperature. The sustainable chemical technology of electron transport and switching materials in semiconductor manufacturing and the development of devices with new unconventional nanophysics, improved performance, and augmented functionalities (beyond-CMOS and More-than-Moore) is becoming increasingly important in the context of a gradual transition to a future-oriented concept of Internet of Everything (IoE). In this article, we focus on the technological significance of semiconductor preparation from single-source (molecular) precursors and the prospect of functionalizing semiconductors using DNA origami nanotechnology and stimuli-responsive metal–oxygen cluster ions such as polyoxometalates (POMs). We also describe the advanced characterization of these qualified molecular systems by soft X-rays. We emphasize the technical relevance of using solution-based methods for the bottom-up preparation of novel and hybrid semiconductors as well as their challenging scalability and the compatibility of methods of molecular technology with lithography-based mass production. Our article aims to contribute to the achievement of the United Nations' Sustainable Development Goal 9 (Industry, Innovation and Infrastructure). [ABSTRACT FROM AUTHOR]

Abstract Self-assembling DNA nanoparticles have the potential to significantly advance the targeted delivery of molecular cargo owing to their chemical and architectural flexibility. Recently, it has been demonstrated that the genetic code embedded in DNA nanoparticles produced by the method of DNA origami or related techniques can be recognized and copied by RNA polymerase in vitro. Further, sculpted DNA nanoparticles can serve as a substrate for Cas9-mediated gene modification and gene expression in cell culture. In the present study, we further investigate the ability of DNA origami nanoparticles to be expressed in a human cell line with emphasis on the impact of single-stranded DNA (ssDNA) domains and the contributions of the architectural disposition of genetic control elements, namely promoter and enhancer sequences. Our findings suggest that while cells possess the remarkable capability to express genes within highly folded architectures, the presence and relative density and location of ssDNA domains appears to influence overall levels of gene expression. These results suggest that it may be possible to nuance folded DNA nanoparticle architecture to regulate the rate and/or level of gene expression. Considering the highly malleable architecture and chemistry of self-assembling DNA nanoparticles, these findings motivate further exploration of their potential as an economic nanotechnology platform for targeted gene editing, nucleic acid-based vaccines, and related biotherapeutic applications.

In recent years, DNA origami-based nanocarriers have been extensively utilized for efficient cancer therapy. However, developing a nanocarrier capable of effectively protecting cargos such as RNA remains a challenge. In this study, we designed a compact and controllable DNA tubular origami (DTO) measuring 120 nm in length and 18 nm in width. The DTO exhibited appropriate structural characteristics for encapsulating and safeguarding cargo. Inside the DTO, we incorporated 20 connecting points to facilitate the delivery of cargoes to various ovarian and normal epithelial cell lines. Specifically, fluorescent-labeled DNA strands were attached to these sites as cargoes. The DTO was engineered to open upon encountering miR-21 through RNA/DNA strand displacement. Significantly, for the first time, we inhibited fluorescence using the compact DNA nanotube and observed dynamic fluorescent signals, indicating the controllable opening of DTO through live-cell imaging. Our results demonstrated that the DTO remained properly closed, exhibited effective internalization in ovarian cancer cells in vitro, showcasing marked differential expression of miR-21, and efficiently opened with short-term exposure to miR-21. Leveraging its autonomous behavior and compact design, the DTO emerges as a promising nanocarrier for various clinically relevant materials. It holds significant application prospects in anti-cancer therapy and the development of flexible biosensors.

Abstract Staphylococcus aureus (SA) poses a serious risk to human and animal health, necessitating a low-cost and high-performance analytical platform for point-of-care diagnostics. Cellulose paper-based field-effect transistors (FETs) with RNA-cleaving DNAzymes (RCDs) can fulfill the low-cost requirements, however, its high hydrophilicity and lipophilicity hinder biochemical modification and result in low sensitivity, poor mechanical stability and poor fouling performance. Herein, we proposed a controllable self-cleaning FET to simplify biochemical modification and improve mechanical stability and antifouling performance. Then, we constructed an RCD-based DNA nanotree to significantly enhance the sensitivity for SA detection. For controllable self-cleaning FET, 1 H,1 H,2 H,2 H-perfluorodecyltrimethoxysilane based-polymeric nanoparticles were synthesized to decorate cellulose paper and whole carbon nanofilm wires. O2 plasma was applied to regulate to reduce fluorocarbon chain density, and then control the hydrophobic-oleophobic property in sensitive areas. Because negatively charged DNA affected the sensitivity of semiconducting FETs, three Y-shaped branches with low-cost were designed and applied to synthesize an RCD-based DNA-Nanotree based on similar DNA-origami technology, which further improved the sensitivity. The trunk of DNA-Nanotree was composed of RCD, and the canopy was self-assembled using multiple Y-shaped branches. The controllable self-cleaning FET biosensor was applied for SA detection without cultivation, which had a wide linear range from 1 to 105 CFU/mL and could detect a low value of 1 CFU/mL.

RNA-based therapeutics have emerged as a promising approach for the treatment of various diseases, including cancer, genetic disorders, and infectious diseases. However, the delivery of RNA molecules into target cells has been a major challenge due to their susceptibility to degradation and inefficient cellular uptake. To overcome these hurdles, DNA-based nano technology offers an unprecedented opportunity as a potential delivery platform for RNA therapeutics. Due to its excellent characteristics such as programmability and biocompatibility, these DNA-based nanostructures, composed of DNA molecules assembled into precise and programmable structures, have garnered significant attention as ideal building materials for protecting and delivering RNA payloads to the desired cellular destinations. In this review, we highlight the current progress in the design and application of three DNA-based nanostructures: DNA origami, lipid-nanoparticle (LNP) technology related to frame guided assembly (FGA), and DNA hydrogel for the delivery of RNA molecules. Their biomedical applications are briefly discussed and the challenges and future perspectives in this field are also highlighted.

An ion detection device that combines a DNA-origami nanopore and a field-effect transistor (FET) was designed and modeled to determine sensitivity of the nanodevice to the local cellular environment. Such devices could be integrated into a live cell, creating an abiotic-biotic interface integrated with semiconductor electronics. A continuum model is used to describe the behavior of ions in an electrolyte solution. The drift-diffusion equations are employed to model the ion distribution, taking into account the electric fields and concentration gradients. This was matched to the results from electric double layer theory to verify applicability of the model to a bio-sensing environment. The FET device combined with the nanopore is shown to have high sensitivity to ion concentration and nanopore geometry, with the electrical double layer behavior governing the device characteristics. A logarithmic relationship was found between ion concentration and a single FET current, generating up to 200 nA of current difference with a small applied bias. [ABSTRACT FROM AUTHOR]

Plasmonic nanoparticles play a pivotal role in various research areas due to their exceptional optical and thermo‐optical properties, like high spectral tunability and efficient light‐to‐heat conversion. Gold, with its biocompatibility, low cytotoxicity, and tunable resonances , makes gold nanoparticles ideal for photothermal therapies. Geometries, including spheres, core–shells, rods, disks, stars, nanocages, and nanotoroids, are extensively studied, with the gold nanodoughnut emerging as one of the most promising ones due to its ability to produce high temperatures and rotational stability. Nevertheless, the fabrication of metallic toroidal shapes remains a challenge. Recent advances in DNA‐based nanotechnology, especially DNA‐origami techniques, provide feasible route for the fabrication of this geometry through metallization reactions or attachment of metal nanoparticles. However, particles manufactured using this method possess a DNA core that influences their thermoplasmonic performance. In this work, a theoretical investigation is conducted on the thermoplasmonic response of DNA‐origami‐based core/shell toroids (CSTs) for photothermal applications. Key parameters that optimize the CST thermoplasmonic response are identified, and compared with their solid counterparts and discrete metallic coatings. Additionally, the CSTs tolerance to random rotations is assessed, providing insights into their behavior in fluidic environments and implications for its practical consideration. [ABSTRACT FROM AUTHOR]

Plasmonic nanomaterials bearing targeting ligands are of great interest for surface‐enhanced Raman scattering (SERS)‐based bioimaging applications. However, the practical utility of SERS‐based imaging strategies is hindered by the lack of a straightforward method to synthesize highly sensitive SERS‐active nanostructures with high yield and efficiency. In this work, leveraging DNA origami principles, the first‐in‐class design of a SERS‐based plasmonically coupled nanoprobe for targeted cancer imaging (SPECTRA) is reported. The nanoprobe harnesses a cancer cell targeting DNA aptamer sequence and vibrational tag with stretching frequency in the cell‐silent Raman window. Through the integration of aptamer sequence specific for DU145 cells, the unique capabilities of SPECTRA for targeted imaging of DU145 cells are shown. The results demonstrate that the scalability, cost‐effectiveness, and reproducibility of this method of fabrication of SERS nanoprobes can serve as a versatile platform for creating nanoprobes with broad applications in the fields of cancer biology and biomedical imaging. [ABSTRACT FROM AUTHOR]

DNA nanostructures exhibit versatile geometries and possess sophisticated capabilities not found in other nanomaterials. They serve as customizable nanoplatforms for orchestrating the spatial arrangement of molecular components, such as biomolecules, antibodies, or synthetic nanomaterials. This is achieved by incorporating oligonucleotides into the design of the nanostructure. In the realm of drug delivery to cancer cells, there is a growing interest in active targeting assays to enhance efficacy and selectivity. The active targeting approach involves a "key‐lock" mechanism where the carrier, through its ligand, recognizes specific receptors on tumor cells, facilitating the release of drugs. Various DNA nanostructures, including DNA origami, Tetrahedral, nanoflower, cruciform, nanostar, nanocentipede, and nanococklebur, can traverse the lipid layer of the cell membrane, allowing cargo delivery to the nucleus. Aptamers, easily formed in vitro, are recognized for their targeted delivery capabilities due to their high selectivity for specific targets and low immunogenicity. This review provides a comprehensive overview of recent advancements in the formation and modification of aptamer‐modified DNA nanostructures within drug delivery systems. [ABSTRACT FROM AUTHOR]

The finite periodic arrangement of functional nanomaterials on the two‐dimensional scale enables the integration and enhancement of individual properties, making them an important research topic in the field of tuneable nanodevices. Although layer‐controllable lattices such as graphene have been successfully synthesized, achieving similar control over colloidal nanoparticles remains a challenge. DNA origami technology has achieved remarkable breakthroughs in programmed nanoparticle assembly. Based on this technology, we proposed a hierarchical assembly strategy to construct a universal DNA origami platform with customized layer properties, which we called 2.5‐dimensional (2.5D) DNA origami crystals. Methodologically, this strategy divides the assembly procedure into two steps: 1) array synthesis, and 2) lattice synthesis, which means that the layer properties, including layer number, interlayer distance, and surface morphology, can be flexibly customized based on the independent designs in each step. In practice, these synthesized 2.5D crystals not only pioneer the expansion of the DNA origami crystal library to a wider range of dimensions, but also highlight the technological potential for templating 2.5D colloidal nanomaterial lattices. [ABSTRACT FROM AUTHOR]

The label-free, non-destructive information provided by Raman spectroscopy regarding chemical composition, molecular structure, and molecular interaction makes it a potent analytical tool. Raman scattering's low intensity, however, prevents it from being widely used in a variety of sectors. Plasmonic nanoparticles (NPs) on the surface may considerably improve the Raman process, resulting in surface-enhanced Raman scattering (SERS). Due to the capacity to co-assembling many particles in complicated shapes with fine control of stoichiometry, orientation, and gaps between the particles, the creation of plasmonic nanostructures utilizing a bottom-up method using DNA origami has generated considerable scientific interest. We evaluate current developments in the use of DNA origami structures for the creation of SERS-based sensors in this review paper. We go through SERS fundamentals, plasmonic enhancement processes, and several plasmonic nanostructure fabrication techniques. Additionally, we discuss the benefits of DNA origami in the construction of plasmonic NPs and the creation of SERS hotspots for analytical and medicinal uses. We also discuss potential paths for future research and difficulties facing DNA origami-based SERS sensors. This study attempts to provide a thorough grasp of DNA origami's potential in the creation of SERS-based sensors and its possibilities for the future. [ABSTRACT FROM AUTHOR]

Nucleic acid aptamers, often termed "chemical antibodies," are short, single‐stranded DNA or RNA molecules, which are selected by SELEX. In addition to their high specificity and affinity comparable to traditional antibodies, aptamers have numerous unique advantages such as wider identification of targets, none or low batch‐to‐batch variations, versatile chemical modifications, rapid mass production, and lack of immunogenicity. These characteristics make aptamers a promising recognition probe for scientific research or even clinical application. Aptamer‐functionalized nanomaterials are now emerged as a promising drug delivery system for various diseases with decreased side‐effects and improved efficacy. In this review, the technological strategies for generating high‐affinity and biostable aptamers are introduced. Moreover, the development of aptamers for their application in biomedicine including aptamer‐based biosensors, aptamer–drug conjugates and aptamer functionalized nanomaterials is comprehensively summarized. [ABSTRACT FROM AUTHOR]

While vaccines have been highly successful in protecting against various infections, there are still many high-priority pathogens for which there are no clinically approved formulations. To overcome this challenge, researchers have explored the use of nanoparticulate strategies for more effective antigen delivery to the immune system. Along these lines, nanotoxoids are a promising biomimetic platform that leverages cell membrane coating technology to safely deliver otherwise toxic bacterial antigens in their native form for antivirulence vaccination. Here, in order to further boost their immunogenicity, nanotoxoids formulated against staphylococcal α-hemolysin are embedded into a DNA-based hydrogel with immunostimulatory CpG motifs. The resulting nanoparticle-hydrogel composite is injectable and improves the in vivo delivery of vaccine antigens while simultaneously stimulating nearby immune cells. This leads to elevated antibody production and stronger antigen-specific cellular immune responses. In murine models of pneumonia and skin infection caused by methicillin-resistant Staphylococcus aureus, mice vaccinated with the hybrid vaccine formulation are well-protected. This work highlights the benefits of combining nanoparticulate antigen delivery systems with immunostimulatory hydrogels into a single platform, and the approach can be readily generalized to a wide range of infectious diseases.

DNA origami nanostructures are promising carries for drug delivery applications. However, their limited stability under relevant conditions often presents a challenge. Herein, the structural stability of DNA origami nanostructures is investigated in a setting compatible with their application in photodynamic therapy (PDT). To this end, DNA origami triangles and six‐helix bundles (6HBs) are loaded with the clinically tested photosensitizer methylene blue, which upon irradiation with red light generates reactive oxygen species (ROS) that attack the DNA origami nanostructures. ROS‐induced structural damage is observed to depend on the ionic composition of the surrounding medium and becomes more severe at low ionic strength. Mg2+ ions can efficiently protect the DNA origami nanostructures from ROS‐induced damage and may even heal some of the damage obtained under Mg2+‐free conditions when added after irradiation. Finally, the employed DNA origami 6HBs are more resistant toward ROS‐induced structural damage than the triangles, which is attributed to their markedly different mechanical properties. These results thus provide some fundamental insights into the stabilizing role of DNA origami superstructure that may guide the selection or design of DNA origami nanocarriers with optimized stability for their application in PDT.

Advancements in cancer immunotherapy have been notable; however, challenges remain regarding precision and the capacity to generate robust immune responses. This review explores the potential of DNA origami, an innovative method for structuring DNA into complex forms, as a platform for advanced cancer vaccines. DNA origami enables precise control over the molecular arrangement on its surface. Researchers can precisely modulate the immune response by conjugating tumor-specific antigens and adjuvants to DNA origami nanocarriers. This targeted approach demonstrates significant promise in overcoming the shortcomings of existing immunotherapies. This may enhance vaccine efficacy by facilitating the efficient delivery of antigens and adjuvants to immune cells. The precise control of adjuvant placement can minimize unnecessary immune stimulation and reduce unwanted side effects. The modular structure of DNA origami facilitates the development of personalized vaccines aimed at targeting specific mutations present in a patient's tumor. This advancement offers significant potential for bringing in a new era of precise cancer therapy. DNA origami nanocarriers demonstrate significant potential in enhancing the safety, efficacy, and precision of cancer immunotherapies.

DNA origami nanodevices achieve programmable structure and tunable mechanical and dynamic properties by leveraging the sequence‐specific interactions of nucleic acids. Previous advances have also established DNA origami as a useful building block to make well‐defined micron‐scale structures through hierarchical self‐assembly, but these efforts have largely leveraged the structural features of DNA origami. The tunable dynamic and mechanical properties also provide an opportunity to make assemblies with adaptive structures and properties. Here the integration of DNA origami hinge nanodevices and coiled‐coil peptides are reported into hybrid reconfigurable assemblies. With the same dynamic device and peptide interaction, it is made multiple higher‐order assemblies (i.e., polymorphic assembly) by organizing clusters of peptides into patches or arranging single peptides into patterns on the surfaces of DNA origami to control the relative orientation of devices. The coiled‐coil interactions are used to construct circular and linear assemblies whose structure and mechanical properties can be modulated with DNA‐based reconfiguration. Reconfiguration of linear assemblies leads to micron scale motions and ≈2.5‐10‐fold increase in bending stiffness. The results provide a foundation for stimulus‐responsive hybrid assemblies that can adapt their structure and properties in response to nucleic acid, peptide, protein, or other triggers. [ABSTRACT FROM AUTHOR]

Cells integrate many mechanical and chemical cues to drive cell signalling responses. Because of the complex nature and interdependency of alterations in extracellular matrix (ECM) composition, ligand density, mechanics, and cellular responses it is difficult to tease out individual and combinatorial contributions of these various factors in driving cell behavior in homeostasis and disease. Tuning of material viscous and elastic properties, and ligand densities, in combinatorial fashions would enhance our understanding of how cells process complex signals. For example, it is known that increased ECM mechanics and transforming growth factor beta (TGF‐β) receptor (TGF‐β‐R) spacing/clustering independently drive TGF‐β signalling and associated myofibroblastic differentiation. However, it remains unknown how these inputs orthogonally contribute to cellular outcomes. Here, we describe the development of a novel material platform that combines microgel thin films with controllable viscoelastic properties and DNA origami to probe how viscoelastic properties and nanoscale spacing of TGF‐β‐Rs contribute to TGF‐β signalling and myofibroblastic differentiation. We found that highly viscous materials with non‐fixed TGF‐β‐R spacing promoted increased TGF‐β signalling and myofibroblastic differentiation. This is likely due to the ability of cells to better cluster receptors on these surfaces. These results provide insight into the contribution of substrate properties and receptor localisation on downstream signalling. Future studies allow for exploration into other receptor‐mediated processes. [ABSTRACT FROM AUTHOR]

In recent years, the field of structural DNA nanotechnology has advanced rapidly due to transformative design tools. Although these tools have been revolutionary, they still bear one overall limitation of requiring users to fully conceptualize their designs before designing. Recently, a simple computational casting technique was developed using generative optimization strategies to automate the DNA origami nanostructure design. This approach employs a shape annealing algorithm, which creates a formal language of honeycomb nanostructures with shape grammars and drives designs from the language toward a desired configuration using simulated annealing. This initial demonstration of the approach can generate novel scaffold routing schemes for creating solid or hollow structures constrained by the boundaries of polyhedral meshes. The results from the initial approach, particularly from the hollow structures, reveal a challenging design space. This simple technique generates novel scaffold routing schemes that do not replicate the overall polyhedral mesh shape and are limited in their ability to control scaffold path exploration in the design space. This paper demonstrates an approach for achieving different levels of consistent effective wall thicknesses and improving the quality of mesh coverage for hollow structures that can be tuned and optimized by introducing a more refined computational casting technique. We achieve these improvements through changes in the simulated annealing algorithm by adding a Hustin move set algorithm that dynamically adjusts the performance of the overall design and redefining how these hollow designs are articulated. This work illustrates how the technique can navigate a challenging design space to generate effective hollow designs. [ABSTRACT FROM AUTHOR]

Single‐stranded DNA oligonucleotides wrapping on the surface of single‐walled carbon nanotubes (SWCNTs), described as DNA corona, are often used as a dispersing agent for SWCNTs. The uneven distribution of DNA corona along SWCNTs is related to the photoelectric properties and the surface activity of SWCNTs. An ionic strength‐mediated "DNA corona defects" (DCDs) strategy is proposed to acquire an exposed surface of SWCNTs (accessible surface) as large as possible while maintaining good dispersibility via modulating the conformation of DNA corona. By adjusting the solution ionic strength, the DNA corona phase transitioned from an even‐distributed and loose conformation to a locally compact conformation. The resulting enlarged exposed surface of SWCNTs is called DCDs, which provide active sites for molecular adsorption. This strategy is applied for the arrangement of SWCNTs on DNA origami. SWCNTs with ≈11 nm DCD, providing enough space for the adsorption of "capture ssDNA" (≈7 nm width required for 24‐nt) extended from DNA origami structures are fabricated. The DCD strategy has potential applications in SWCNT‐based optoelectronic devices. [ABSTRACT FROM AUTHOR]

Deoxyribonucleic acid (DNA) origami enables the synthesis of bespoke nanoscale structures suitable for diverse applications. Effective design requires preventing uncontrolled aggregation, while still facilitating directed multi‐subunit assembly. Uncontrolled aggregation is often caused by base‐stacking interactions between arrays of blunt‐ended helices, a problem which is typically mitigated by incorporating disordered single‐stranded DNA (ssDNA) (like scaffold loops or poly‐thymine brushes) at the end of double‐stranded DNA (dsDNA) helices. Such disordered regions are ubiquitous in DNA origami structures yet their optimal design requirements in various chemical environments remains unclear. This study systematically investigates scaffold loops and poly‐nucleotide brushes for aggregation prevention and control of multi‐subunit assembly, examining length, sequence, and MgCl2 concentration dependencies. Additionally, a novel strategy is introduced using orthogonal double‐stranded DNA helices to create a steric shield against base stacking. The results reveal key considerations. Poly‐thymine brushes excel in achieving monodispersity across diverse conditions whereas scaffold loops aid directed multi‐subunit assembly. Orthogonal DNA helices remove the need for disordered regions altogether, preventing aggregation over a broad range of MgCl2 concentrations and facilitating controlled multi‐subunit assembly. This study expands the toolbox for DNA origami design and enables a more informed approach for achieving control of monodispersity and multi‐subunit assembly in DNA origami structures. [ABSTRACT FROM AUTHOR]

Plasmonic nanoparticles play a pivotal role in various research areas due to their exceptional optical and thermo‐optical properties, like high spectral tunability and efficient light‐to‐heat conversion. Gold, with its biocompatibility, low cytotoxicity, and tunable resonances , makes gold nanoparticles ideal for photothermal therapies. Geometries, including spheres, core–shells, rods, disks, stars, nanocages, and nanotoroids, are extensively studied, with the gold nanodoughnut emerging as one of the most promising ones due to its ability to produce high temperatures and rotational stability. Nevertheless, the fabrication of metallic toroidal shapes remains a challenge. Recent advances in DNA‐based nanotechnology, especially DNA‐origami techniques, provide feasible route for the fabrication of this geometry through metallization reactions or attachment of metal nanoparticles. However, particles manufactured using this method possess a DNA core that influences their thermoplasmonic performance. In this work, a theoretical investigation is conducted on the thermoplasmonic response of DNA‐origami‐based core/shell toroids (CSTs) for photothermal applications. Key parameters that optimize the CST thermoplasmonic response are identified, and compared with their solid counterparts and discrete metallic coatings. Additionally, the CSTs tolerance to random rotations is assessed, providing insights into their behavior in fluidic environments and implications for its practical consideration.

Abstract DNA nanostructures exhibit versatile geometries and possess sophisticated capabilities not found in other nanomaterials. They serve as customizable nanoplatforms for orchestrating the spatial arrangement of molecular components, such as biomolecules, antibodies, or synthetic nanomaterials. This is achieved by incorporating oligonucleotides into the design of the nanostructure. In the realm of drug delivery to cancer cells, there is a growing interest in active targeting assays to enhance efficacy and selectivity. The active targeting approach involves a “key‐lock” mechanism where the carrier, through its ligand, recognizes specific receptors on tumor cells, facilitating the release of drugs. Various DNA nanostructures, including DNA origami, Tetrahedral, nanoflower, cruciform, nanostar, nanocentipede, and nanococklebur, can traverse the lipid layer of the cell membrane, allowing cargo delivery to the nucleus. Aptamers, easily formed in vitro, are recognized for their targeted delivery capabilities due to their high selectivity for specific targets and low immunogenicity. This review provides a comprehensive overview of recent advancements in the formation and modification of aptamer‐modified DNA nanostructures within drug delivery systems.

Abstract The fabrication of precisely patterned polymers at the nanoscale is of critical importance. We have previously succeeded in creating various nanopatterned polymers with nanoscale resolution through the use of in situ atom transfer radical polymerization (ATRP) techniques on deoxyribonucleic acid (DNA) origami. However, separating nanopatterned polymers from the origami template without damaging the origami presents a significant challenge, thereby increasing costs and limiting the development of applications involving nanopatterned polymers. Here, we achieved spatially and temporally controlled release of DNA origami templates through photo‐regulation by incorporating azobenzene‐modified DNA into the initiator. Under UV exposure, azobenzene isomerization rapidly induces the disassociation of patterned polymers from the origami template at ambient temperatures, without damaging the DNA origami. Additionally, the released origami template can be reused as a template for the cyclic production of nanopatterned polymers. This method provides a pathway for the large‐scale production of patterned polymers at reduced costs and facilitates dynamic control over the polymer‐DNA complex, with potential applications in both the biomedical and chemical fields.

DNA nanostructures are well-established vectors for packaging diversified payloads for targeted cellular delivery. Here, DNA origami rectangular sheets were combined with Herpes Simplex Virus 1 (HSV1) capsids to demonstrate surface coverage of the particle via electrostatic interactions. The optimized origami:HSV1 molar ratios led to characteristic packaging geometries ranging from dispersed HSV1 pockets to agglomerated HSV1 sleeves. Pockets were disguised from cells in HeLa and B16F10 cells and were 44.2% less infective than naked HSV1 particles. However, the pockets were 117% more infective than naked HSV1 particles when the origami sheets were coated with folic acid. We observed infectivity from naked origami, but they are 99.1% less infective with respect to HSV1 and 99.6% less infective with respect to the pocket complexes. This work suggests that DNA origami can selectively modulate virus infectivity.

DNA origami nanostructures are emerging as a bottom-up nanopatterning approach. Direct combination of this approach with top-down nanotechnology, such as ion beams, has not been considered because of the soft nature of the DNA material. Here we demonstrate that the shape of 2D DNA origami nanostructures deposited on Si substrates is well preserved upon irradiation by ion beams, modeling ion implantation, lithography, and sputtering conditions. Structural changes in 2D DNA origami nanostructures deposited on Si are analyzed using AFM imaging. The observed effects on DNA origami include structure height decrease or increase upon fast heavy ion irradiation in vacuum and in air, respectively. Slow- and medium-energy heavy ion irradiation results in the cutting of the nanostructures or crater formation with ion-induced damage in the 10 nm range around the primary ion track. In all these cases, the designed shape of the 2D origami nanostructure remains unperturbed. Present stability and nature of damages on DNA origami nanostructures enable fusion of DNA origami advantages such as shape and positioning control into novel ion beam nanofabrication approaches.

Design strategies for DNA and RNA nanostructures have developed along parallel lines for the past 30 years, from small structural motifs derived from biology to large ‘origami’ structures with thousands to tens of thousands of bases. With the recent publication of numerous RNA origami structures and improved design methods-even permitting co-transcriptional folding of kilobase-sized structures – the RNA nanotechnolgy field is at an inflection point. Here, we review the key achievements which inspired and enabled RNA origami design and draw comparisons with the development and applications of DNA origami structures. We further present the available computational tools for the design and the simulation, which will be key to the growth of the RNA origami community. Finally, we portray the transition from RNA origami structure to function. Several functional RNA origami structures exist already, their expression in cells has been demonstrated and first applications in cell biology have already been realized. Overall, we foresee that the fast-paced RNA origami field will provide new molecular hardware for biophysics, synthetic biology and biomedicine, complementing the DNA origami toolbox.

Origami, the art of paper folding, has long fascinated researchers and designers in its potential to replicate and tap the complexity of nature. In this paper, we pursue the crossing of origami engineering structures and biology, the realm of biologically-inspired origami structures categorized by the two biggest taxonomy kingdoms and DNA origami. Given the diversity of life forms that Earth comprises, we pursue an analysis of biomimetic designs that resemble intricate patterns and functionalities occurring in nature. Our research begins by setting out a taxonomic framework for the classification of origami structures based on biologically important kingdoms. From each of these, we explore the engineering structures inspired by morphological features, behaviors, and ecological adaptations of organisms. We also discuss implications in realms such as sustainability, biomaterials development, and bioinspired robotics. Thus, by parlaying the principles found in nature’s design playbook through the art of folding, biologically inspired origami becomes fertile ground for interdisciplinary collaboration and creativity. Through this approach, we aim to inspire readers, researchers, and designers to embark on a journey of discovery in which the boundaries between art, science, and nature are blurred, providing a foundation for innovation to thrive.

Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and concentrations of subunits. By contrast, we introduce an assembly paradigm that allows large error-tolerance in the subunit affinity and helps avoid kinetic traps. Our combined experimental and computational approach uses a model system of triangular subunits programmed to assemble into T = 3 icosahedral capsids comprising 60 units. The experimental platform uses DNA origami to create monodisperse colloids whose three-dimensional geometry is controlled to nanometer precision, with two distinct bonds whose affinities are controlled to kBT precision, quantified in situ by static light scattering. The computational model uses a coarse-grained representation of subunits, short-ranged potentials, and Langevin dynamics. Experimental observations and modeling reveal that when the bond affinities are unequal, two distinct hierarchical assembly pathways occur, in which the subunits first form dimers in one case and pentamers in another. These hierarchical pathways produce complete capsids faster and are more robust against affinity variation than egalitarian pathways, in which all binding sites have equal strengths. This finding suggests that hierarchical assembly may be a general engineering principle for optimizing self-assembly of complex target structures. [ABSTRACT FROM AUTHOR]

There have been limited efforts to ligate the staple nicks in DNA origami which is crucial for their stability against thermal and mechanical treatments, and chemical and biological environments. Here, two near quantitative ligation methods are demonstrated for the native backbone linkage at the nicks in origami: i) a cosolvent dimethyl sulfoxide (DMSO)‐assisted enzymatic ligation and ii) enzyme‐free chemical ligation by CNBr. Both methods achieved over 90% ligation in 2D origami, only CNBr‐method resulted in ≈80% ligation in 3D origami, while the enzyme‐alone yielded 31–55% (2D) or 22–36% (3D) ligation. Only CNBr‐method worked efficiently for 3D origami. The CNBr‐mediated reaction is completed within 5 min, while DMSO‐method took overnight. Ligation by these methods improved the structural stability up to 30 °C, stability during the electrophoresis and subsequent extraction, and against nuclease and cell lysate. These methods are straightforward, non‐tedious, and superior in terms of cost, reaction time, and efficiency. [ABSTRACT FROM AUTHOR]

DNA nanostructures have played an important role in the development of novel drug delivery systems. Herein, we report a DNA origami‐based CRISPR/Cas9 gene editing system for efficient gene therapy in vivo. In our design, a PAM‐rich region precisely organized on the surface of DNA origami can easily recruit and load sgRNA/Cas9 complex by PAM‐guided assembly and pre‐designed DNA/RNA hybridization. After loading the sgRNA/Cas9 complex, the DNA origami can be further rolled up by the locking strands with a disulfide bond. With the incorporation of DNA aptamer and influenza hemagglutinin (HA) peptide, the cargo‐loaded DNA origami can realize the targeted delivery and effective endosomal escape. After reduction by GSH, the opened DNA origami can release the sgRNA/Cas9 complex by RNase H cleavage to achieve a pronounced gene editing of a tumor‐associated gene for gene therapy in vivo. This rationally developed DNA origami‐based gene editing system presents a new avenue for the development of gene therapy. [ABSTRACT FROM AUTHOR]

Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A‐motif—protonated, self‐complementary poly(adenine) sequences—can propagate DNA origami into one‐dimensional, micron‐length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils. This system is recyclable and does not require DNA modification. By employing a modular and waste‐free strategy to assemble and disassemble hierarchical structures built from DNA origami, we offer a facile and accessible route to developing well‐defined, dynamic, and large DNA assemblies with temporal control. As a general tool, we envision that coupling the A‐motif to cycles of dissipative protonation will allow the transient construction of diverse DNA nanostructures, finding broad applications in dynamic and non‐equilibrium nanotechnology. [ABSTRACT FROM AUTHOR]

Alongside other players, such as CpG methylation and the "histone code," transcription factors (TFs) represent a key feature of gene regulation. TFs are implicated in critical cellular processes, ranging from cell death, growth, and differentiation, up to intranuclear signaling of steroid and other hormones, physical entities, and hypoxia regulation. Notwithstanding an extensive body of research in this field, several questions and therapeutic options remain unanswered and unexplored, respectively. Of note, many of these TFs represent therapeutic targets, which are either difficult to be pharmacologically tackled or are still not drugged via traditional approaches, such as small-molecule inhibition. Upon providing a brief overview of TFs, we focus herein on how synthetic biology/medicine could assist in their study as well as their therapeutic targeting. Specifically, we contend that DNA origami, i.e., a novel synthetic DNA nanotechnological approach, represents an excellent synthetic biology/medicine tool to accomplish the above goals, since it can harness several vital characteristics of DNA: DNA polymerization, DNA complementarity, DNA "programmability," and DNA "editability." In doing so, DNA origami can be applied to study TF dynamics during DNA transcription, to elucidate xeno-nucleic acids with distinct scaffolds and unconventional base pairs, and to use TFs as competitors of oncogene-engaged promoters. Overall, because of their potential for high-throughput design and their favorable pharmacodynamic and pharmacokinetic properties, DNA origami can be a novel armory for TF-related drug design. Last, we discuss future trends in the field, such as RNA origami and innovative DNA origami–based therapeutic delivery approaches. [ABSTRACT FROM AUTHOR]

The DNA origami method has revolutionized the field of DNA nanotechnology since its introduction. These nanostructures, with their customizable shape and size, addressability, nontoxicity, and capacity to carry bioactive molecules, are promising vehicles for therapeutic delivery. Different approaches have been developed for manipulating and folding DNA origami, resulting in compact lattice-based and wireframe designs. Platinum-based complexes, such as cisplatin and phenanthriplatin, have gained attention for their potential in cancer and antiviral treatments. Phenanthriplatin, in particular, has shown significant antitumor properties by binding to DNA at a single site and inhibiting transcription. The present work aims to study wireframe DNA origami nanostructures as possible carriers for platinum compounds in cancer therapy, employing both cisplatin and phenanthriplatin as model compounds. This research explores the assembly, platinum loading capacity, stability, and modulation of cytotoxicity in cancer cell lines. The findings indicate that nanomolar quantities of the ball-like origami nanostructure, obtained in the presence of phenanthriplatin and therefore loaded with that specific drug, reduced cell viability in MCF-7 (cisplatin-resistant breast adenocarcinoma cell line) to 33%, while being ineffective on the other tested cancer cell lines. The overall results provide valuable insights into using wireframe DNA origami as a highly stable possible carrier of Pt species for very long time-release purposes. [ABSTRACT FROM AUTHOR]

To assist in the speed and accuracy of designing brick-based DNA nanostructures, we introduce a lightweight software suite 3DNA that can be used to generate complex structures. Currently, implementation of this fabrication strategy involves working with generalized, typically commercial CAD software, ad-hoc sequence-generating scripts, and visualization software, which must often be integrated together with an experimental lab setup for handling the hundreds or thousands of constituent DNA sequences. 3DNA encapsulates the solutions to these challenges in one package by providing a customized, easy-to-use molecular canvas and back-end functionality to assist in both visualization and sequence design. The primary motivation behind this software is enabling broader use of the brick-based method for constructing rigid, 3D DNA-based nanostructures, first introduced in 2012. 3DNA is developed to provide a streamlined, real-time workflow for designing and implementing this type of 3D nanostructure by integrating different visualization and design modules. Due to its cross-platform nature, it can be used on the most popular desktop environments, i.e., Windows, Mac OS X, and various flavors of Linux. 3DNA utilizes toolbar-based navigation to create a user-friendly GUI and includes a customized feature to analyze the constituent DNA sequences. Finally, the oligonucleotide sequences themselves can either be created on the fly by a random sequence generator, or selected from a pre-existing set of sequences making up a larger molecular canvas. [ABSTRACT FROM AUTHOR]