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The evolution of dynamic DNA nanostructures has propelled DNA nanotechnology into a robust and versatile field, offering groundbreaking applications in nanoscale communication, drug delivery, and molecular computing. Yet, the full potential of this technology awaits further enhancement through optimization of kinetic properties governing conformational changes. In this work, we introduce a mean-field theory to characterize the kinetic behavior of a dynamic DNA origami hinge where each arm bears complementary single-stranded DNA overhangs of different lengths, which can latch the hinge at a closed conformation. This device is currently being investigated for multiple applications, being of particular interest the development of DNA-based rapid diagnostic tests for coronavirus. Drawing from classical statistical mechanics theories, we derive analytical expressions for the mean binding time of these overhangs within a constant hinge. This analysis is then extended to flexible hinges, where the angle diffuses within a predetermined energy landscape. We validate our model by comparing it with experimental measurements of the closing rates of DNA nanocalipers with different energy landscapes and overhang lengths, demonstrating excellent agreement and suggesting fast angular relaxation relative to binding. These findings offer insights that can guide the optimization of devices for specific state lifetimes. Moreover, the framework introduced here lays the groundwork for further advancements in modeling the kinetics of dynamic DNA nanostructures. [ABSTRACT FROM AUTHOR]

The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales and system sizes involved. In this article, we present a new coarse-grained model for investigating the folding dynamics of nucleic acids. Our model represents three nucleotides with a patchy particle and is parameterized using well-established nearest-neighbor models. Thanks to the reduction of degrees of freedom and to a bond-swapping mechanism, our model allows for simulations at timescales and length scales that are currently inaccessible to more detailed models. To validate the performance of our model, we conducted extensive simulations of various systems: We examined the thermodynamics of DNA hairpins, capturing their stability and structural transitions, the folding of an MMTV pseudoknot, which is a complex RNA structure involved in viral replication, and also explored the folding of an RNA tile containing a k-type pseudoknot. Finally, we evaluated the performance of the new model in reproducing the melting temperatures of oligomers and the dependence on the toehold length of the displacement rate in toehold-mediated displacement processes, a key reaction used in molecular computing. All in all, the successful reproduction of experimental data and favorable comparisons with existing coarse-grained models validate the effectiveness of the new model. [ABSTRACT FROM AUTHOR]

Reconfigurable chiral plasmonic complexes are fabricated by planar assembly of multiple individual gold nanorod dimers using DNA origami templates. Additionally, each chiral center can be controlled to switch among achiral, left-handed, and right-handed states. We demonstrate that their overall circular dichroism is determined by the coupling of individual chiral centers and is heavily influenced by the precise number and arrangement of these centers. Our study offers a novel self-assembly method for constructing intricate and dynamic chiral plasmonics as well as investigating the interactions among several plasmonic chiral centers. [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]

DNA conformations, which encompass the three-dimensional structures of the DNA strand, play a crucial role in genome regulation. During DNA translocation in a nanopore, various conformations occur due to interactions among force fields, the fluidic environment, and polymer features. The most common conformation is folding, where DNA moves through the nanopore in a two-strand or multi-strand manner, influencing the current signature. Factors such as hydrodynamic drag, ionic environments, and DNA length significantly affect these conformations. Notably, conical nanopores, with their asymmetrical geometry, impose unique constraints on DNA translocation. Our findings reveal that during forward translocation, from the narrow (cis) end to the wide (trans) end, DNA experiences less resistance, resulting in shorter translocation times and higher blockade currents. Conversely, backward translocation, from the wide (trans) end to the narrow (cis) end, leads to longer translocation times and more complex conformations due to increased hydrodynamic drag and geometric constraints. This study employs molecular ping-pong methods to confine DNA, further highlighting the intricate dynamics of DNA folding within nanopores. These insights enhance the understanding of DNA behavior in confined environments, contributing to advancements in nanopore-based sensing and sequencing technologies, with implications for genome regulation and biomedical applications. [ABSTRACT FROM AUTHOR]

Purine stretches, sequences of adenine (A) and guanine (G) in DNA, play critical roles in binding regulatory protein factors and influence gene expression by affecting DNA folding. This study investigates the relationship between purine stretches and cancer development, considering the aromaticity of purines, quantified by methods like Hückel's rule and NICS calculations, and the importance of the flanking sequence context. A pronounced avoidance of long purine stretches by typical cancer mutations was observed in public data on the intergenic regions of cancer patients, suggesting a role of intergenic sequences in chromatin reorganization and gene regulation. A statistically significant shortening of purine stretches in cancerous tumors (p value < 0.0001) was found. The insights into the aromatic nature of purines and their stacking energies explain the role of purine stretches in DNA structure, contributing to their role in cancer progression. This research lays the groundwork for understanding the nature of purine stretches, emphasizing their importance in gene regulation and chromatin restructuring, and offers potential avenues for novel cancer therapies and insights into cancer etiology. [ABSTRACT FROM AUTHOR]

Deoxyribonucleic acid (DNA) is able to form non-canonical four-stranded helical structures with diverse folding patterns known as G-quadruplexes (G4s). G4 topologies are classified based on their relative strand orientation following the 5' to 3' phosphate backbone polarity. Broadly, G4 topologies are either parallel (4+0), antiparallel (2+2), or hybrid (3+1). G4s play crucial roles in biological processes such as DNA repair, DNA replication, transcription and have thus emerged as biological targets in drug design. While computational models have been developed to predict G4 formation, there is currently no existing model capable of predicting G4 folding topology based on its nucleic acid sequence. Therefore, we introduce G4ShapePredictor (G4SP), an application featuring a collection of multi-classification machine learning models that are trained on a custom G4 dataset combining entries from existing literature and in-house circular dichroism experiments. G4ShapePredictor is designed to accurately predict G4 folding topologies in potassium ( K + ) buffer based on its primary sequence and is able to incorporate a threshold optimization strategy allowing users to maximise precision. Furthermore, we have identified three topological sequence motifs that suggest specific G4 folding topologies of (4+0), (2+2) or (3+1) when utilising the decision-making mechanisms of G4ShapePredictor. [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]

Chimeric antigen receptor (CAR) T-cell therapies have shown remarkable results in patients with hematological malignancies. However, their success in treating solid tumors has been limited. As an alternative candidate for the CAR therapy, CAR-macrophages (CAR-M) have demonstrated activation and phagocytosis directed by tumor-associated antigen (TAA), showing promise in the treatment of solid tumors. Nevertheless, the mechanisms by which CARs direct tumor chemotaxis and invasion of CAR-M remain poorly understood. In this study, we aim to investigate the role of CARs in CAR-M attachment and infiltration using 3D tumor spheroids, which were created by utilizing a novel self-assembling nucleic acid nanostructure decorated living cells (NAC). Our results demonstrated that CAR-M exhibited higher invasion and killing capacity in 2D model and 3D tumor spheroids. In summary, the 3D NAC assembled tumor spheroid model provides a suitable platform for target screening and pharmacodynamic evaluation of CAR-M. A novel self-assembled nucleic acid nanostructure-fabricated three-dimensional tumor sphere demonstrates potential for target screening and pharmacodynamic evaluation of CAR-M therapies. [ABSTRACT FROM AUTHOR]

DNAzymes, a class of single-stranded catalytic DNA with good stability, high catalytic activity, and easy synthesis, functionalization and modification properties, have garnered significant interest in the realm of biosensing and bioimaging. Their integration with fluorescent dyes or chemiluminescent moieties has led to remarkable bioimaging outcomes, while DNAzyme-based biosensors have demonstrated robust sensitivity and selectivity in detecting metal ions, nucleic acids, proteins, enzyme activities, exosomes, bacteria and microorganisms. In addition, by delivering DNAzymes into tumor cells, the mRNA therein can be cleaved to regulate the expression of corresponding proteins, which has further propelled the application of DNAzymes in cancer gene therapy and synergistic therapy. This paper reviews the strategies for screening attractive DNAzymes such as SELEX and high-throughput sequencing, and briefly describes the amplification strategies of DNAzymes, which mainly include catalytic hairpin assembly (CHA), DNA walker, hybridization chain reaction (HCR), DNA origami, CRISPR-Cas12a, rolling circle amplification (RCA), and aptamers. In addition, applications of DNAzymes in bioimaging, biosensing, and cancer therapy are also highlighted. Subsequently, the possible challenges of these DNAzymes in practical applications are further pointed out, and future research directions are suggested. [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]

Early lung cancer screening by computed tomography is hampered by pulmonary nodules caused by massive COVID‐19 infections, necessitating an ultrasensitive approach for the early diagnosis of lung cancers at the single‐base level from circular tumor DNAs (ctDNAs). This study introduces an approach that merges DNA origami and DNA scissors technologies in a framework of surface plasmon resonance (SPR) biosensors. By combining the precision of DNA origami probes with the inherent single‐base resolution of DNA scissors, this method systematically addresses the limitations of conventional SPR techniques, resulting in enhanced detection accuracy. The synergistic interplay between DNA scissors and DNA origami enables the SPR biosensors to achieve unprecedented levels of sensitivity, precision, and practical utility. This efficacy allows the precise identification of mutations, demonstrated here by detection of the T790M mutation in the EGFR gene and the G12C mutation in the KRAS gene of non‐small cell lung cancer patients. With this technique, single‐base resolution as well as near zeptomolar‐level sensitivity is achieved. As a result, this discovery holds significant potential to advance the field of precision diagnostics. [ABSTRACT FROM AUTHOR]

DNA nanostructures have been regarded as promising platforms for molecular information coding for their high programmability and nanoscale addressability. However, steganography based on DNA nanostructures still needs further investigation. Here, we designed and synthesized a coumarin derivative structure with selective photo responsiveness in the visible light spectrum and developed a DNA origami steganography system that can only be decrypted through specific light exposure conditions. Under right light treatment, the effective cleavage of photoresponsive groups would cause some of the streptavidin binding sites to detach from the origami, thereby allowing the steganographic information to be read correctly. [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]

With recent advances in multi-color super-resolution light microscopy, it is possible to simultaneously visualize multiple subunits within biological structures at nanometer resolution. To optimally evaluate and interpret spatial proximity of stainings on such an image, colocalization analysis tools have to be able to integrate prior knowledge on the local geometry of the recorded biological complex. We present MultiMatch to analyze the abundance and location of chain-like particle arrangements in multi-color microscopy based on multi-marginal optimal unbalanced transport methodology. Our object-based colocalization model statistically addresses the effect of incomplete labeling efficiencies enabling inference on existent, but not fully observable particle chains. We showcase that MultiMatch is able to consistently recover existing chain structures in three-color STED images of DNA origami nanorulers and outperforms geometry-uninformed triplet colocalization methods in this task. MultiMatch generalizes to an arbitrary number of color channels and is provided as a user-friendly Python package comprising colocalization visualizations. MultiMatch performs geometry-informed colocalization analysis for multi-color microscopy based on multi-marginal optimal unbalanced transport methodology. [ABSTRACT FROM AUTHOR]

Allostery is a hallmark of cellular function and important in every biological system. Still, we are only starting to mimic it in the laboratory. Here, we introduce an approach to study aspects of allostery in artificial systems. We use a DNA origami domino array structure which–upon binding of trigger DNA strands–undergoes a stepwise allosteric conformational change. Using two FRET probes placed at specific positions in the DNA origami, we zoom in into single steps of this reaction cascade. Most of the steps are strongly coupled temporally and occur simultaneously. Introduction of activation energy barriers between different intermediate states alters this coupling and induces a time delay. We then apply these approaches to release a cargo DNA strand at a predefined step in the reaction cascade to demonstrate the applicability of this concept in tunable cascades of mechanochemical coupling with both spatial and temporal control. Allostery is a hallmark of cellular function and important in every biological system, but difficult to artificially mimic. Here, the authors report an approach to study aspects of allostery in artificial systems, using a DNA origami domino array structure which, upon binding of trigger DNA strands, undergoes a stepwise allosteric conformational change that can be monitored by a double FRET probe. [ABSTRACT FROM AUTHOR]

DNA nanostructures have shown great potential in biomedical fields. However, the immune responses, especially the activation of the cGAS‐STING signaling (A‐cGSs), induced by DNA nanostructures, remain incompletely understood. Here, the ability of various DNA nanostructures from double‐stranded DNA (dsDNA), single‐stranded tiles (SSTs) to DNA origami is investigated on A‐cGSs. Unlike natural dsDNA which triggers potent A‐cGSs, the structural interconnectivity of various DNA configurations can substantially reduce the occurrence of A‐cGSs, irrespective of their form, dimensions, and conformation. However, wireframe DNA nanostructures can activate the cGAS‐STING signaling, suggesting that decreasing A‐cGSs is dsDNA compactness‐dependent. Based on this, a reconfigurable DNA Origami Domino Array (DODA) is used to systematically interrogate how dsDNA influences the A‐cGSs and demonstrates that the length, number, and space of dsDNA array coordinately influence the activation level of cGAS‐STING signaling, realizing a regulation of innate immune response. The above data and findings enhance the understanding of how DNA nanostructures affect cellular innate immune responses and new insights into the modulation of innate immune responses by DNA nanomedicine. [ABSTRACT FROM AUTHOR]

Biological channels, especially membrane proteins, play a crucial role in metabolism, facilitating the transport of nutrients and other materials across cell membranes in a bio‐electrolyte environment. Artificial nanopores are employed to study ion and biomolecule transport behavior inside. While the non‐specific interaction between the nanopore surface and transport targets has garnered significant attention, the impact of surface roughness is overlooked. In this study, Nanopores with different levels of inner surface roughness is created by adjusting the FIB (Focus Ion Beam) fabrication parameters. Experiments and molecular dynamics (MD) simulations are employed to demonstrate that greater roughness results from larger FIB beam currents and shorter processing times. Lower roughness increases the capture rate of biomolecules, while greater roughness enhances the normalized blockade current (ΔI/I0). The phenomenon of rougher nanopores are attributed to a barrier‐dominated capture mechanism and more likely to induce DNA folding. This transport barrier exists in rough nanopores by utilizing steer molecular dynamics (SMD) simulations to investigate the force profile of a dA10 DNA molecule during translocation is demonstrated. This work illustrates how surface roughness influences the ionic current features and the translocation of biomolecules, paving a new way for tunning the molecule transport in nanopores. [ABSTRACT FROM AUTHOR]

A single-stranded product scaffold obtained by RCA reaction is woven into an origami-like nano-fence-shaped product (FP) microarray superstructure by only one short bridge strand, circumventing the requirement for a very few viral genome scaffold. Using FP microarray as a template, the two-dimensional protein or nanoparticle patterns can be assembled in a precise and programmable manner, exhibiting the potential applications such as biomedical engineering, therapy, nanophotonics and electronics. [Display omitted] The universal programmed construction of patterned periodic self-assembled nanostructures is a technical challenge in DNA origami nanotechnology but has numerous potential applications in biotechnology and biomedicine. In order to circumvent the dilemma that traditional DNA origami requires a long unusual single-stranded virus DNA as the scaffold and hundreds or even thousands of short strands as staples, we report a method for constructing periodically-self-folded rolling circle amplification products (RPs). The repeating unit is designed to have 3 intra-unit duplexes (inDP1,2,3) and 2 between-unit duplexes (buDP1,2). Based on the complementary pairing of bases, RPs each can self-fold into a periodic grid-patterned ribbon (GR) without the help of any auxiliary oligonucleotide staple. Moreover, by using only an oligonucleotide bridge strand, the GRs are connected together into the larger and denser planar nano-fence-shaped product (FP), which substantially reduces the number of DNA components compared with DNA origami and eliminates the obstacles in the practical application of DNA nanostructures. More interestingly, the FP-based DNA framework can be easily functionalized to offer spatial addressability for the precise positioning of nanoparticles and guest proteins with high spatial resolution, providing a new avenue for the future application of DNA assembled framework nanostructures in biology, material science, nanomedicine and computer science that often requires the ordered organization of functional moieties with nanometer-level and even molecular-level precision. [ABSTRACT FROM AUTHOR]

In this study, the models for the DNA origami lattice will be investigated. Our aim is to theoretically explore the ways of constructing DNA origami. To achieve this goal the DNA origami structure, consisting of nanowires embedded in a host material, will be treated from the perspective of nanowire metamaterial. Surface plasmon polaritons propagating at the interface of air and DNA metamaterial are analyzed. The dispersion relation is attained using the transfer matrix technique and employing continuity conditions of electric fields and their derivatives at the boundary separating two regions. We have concluded that with numerous nanowires into the metamaterial unit, cell frequencies of surface plasmon polaritons are altered to higher frequencies. In this study, we have studied the effect of modifications of the metamaterial, allowing for the shift of the dispersion maps toward higher frequencies. It is possible to obtain the propagation of spoof plasmons mimicking the behavior of surface waves at lower frequencies. All the properties and parameters of the inorganic metamaterials are applicable to study the phenomenon of the organic substances. [ABSTRACT FROM AUTHOR]

DNA origami nanostructures (DONs) are able to scavenge reactive oxygen species (ROS) and their scavenging efficiency toward ROS radicals was shown to be comparable to that of genomic DNA. Herein, we demonstrate that DONs are highly efficient singlet oxygen quenchers outperforming double‐stranded (ds) DNA by several orders of magnitude. To this end, a ROS mixture rich in singlet oxygen is generated by light irradiation of the photosensitizer methylene blue and its cytotoxic effect on Escherichia coli cells is quantified in the presence and absence of DONs. DONs are found to be vastly superior to dsDNA in protecting the bacteria from ROS‐induced damage and even surpass established ROS scavengers. At a concentration of 15 nM, DONs are about 50 000 times more efficient ROS scavengers than dsDNA at an equivalent concentration. This is attributed to the dominant role of singlet oxygen, which has a long diffusion length and reacts specifically with guanine. The dense packing of the available guanines into the small volume of the DON increases the overall quenching probability compared to a linear dsDNA with the same number of base pairs. DONs thus have great potential to alleviate oxidative stress caused by singlet oxygen in diverse therapeutic settings. [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]

DNA nanostructures, known for their programmability, ease of modification, and favourable biocompatibility, have gained widespread application in the biomedical field. Among them, Tetrahedral DNA Origami (TDOs), as a novel DNA nanostructure, possesses well‐defined structures, multiple modification sites, and large cavities, making it a promising drug carrier. However, current understanding of TDOs' interactions with biological systems, particularly with target cells and organs, remains unexplored, limiting its further applications in biomedicine. In this work, we prepared TDOs with an average particle size of 40 nm and labelled them with Cy5 fluorescent molecules. Following intravenous injection in mice, the uptake of TDOs by different types of liver and kidney cells was observed. Results indicated that TDOs accumulate in renal tubules and are metabolized by Kupffer cells, epithelial cells, and hepatocytes in the liver. Additionally, in a tumour‐bearing mouse model, TDOs passively targeted tumour tissues and exhibited excellent tumour penetration and retention after rapid metabolism in hepatocytes. Our findings provide crucial insights for the development of TDO‐based drug delivery systems. [ABSTRACT FROM AUTHOR]

In this study, we developed DNA origami as a multiple module co-delivery carrier for immunotherapy. Three types of immune stimulators were precisely assembled in the nanocarrier. The doxorubicin (DOX) component induced immunogenic cell death (ICD) of tumor cells and enhanced phagocytosis of antigen-presenting cells (APCs). Exogenous double-stranded DNA (dsDNA) could act as a molecular adjuvant to activate the stimulator of interferon genes (STING) signaling in APCs by engulfing dying tumor cells. The interleukin (IL)-12 plasmid and small hairpin programmed cell death-ligand 1 (shPD-L1) transcription template were designed to regulate TME. By modifying targeting moieties (cRGD) and controlled-release groups (disulfide bonds), multi-modules can be released more effectively at the desired site in a controlled manner. [Display omitted] A major challenge in combining cancer immunotherapy is the efficient delivery of multiple types of immunological stimulators to elicit a robust anti-tumor immune response and reprogram the immunosuppressive tumor microenvironment (TME). Here, we developed a DNA nanodevice that was generated by precisely assembling three types of immunological stimulators. The doxorubicin (Dox) component induced immunogenic cell death (ICD) in tumor cells and enhanced phagocytosis of antigen-presenting cells (APCs). Exogenous double-stranded DNA (dsDNA) could act as a molecular adjuvant to activate the stimulator of interferon genes (STING) signaling in APCs by engulfing dying tumor cells. Interleukin (IL)-12 and small hairpin programmed cell death-ligand 1 (shPD-L1) transcription templates were designed to regulate TME. Additionally, for targeted drug delivery, multiple cyclo[Arg-Gly-Asp-(d -Phe)-Cys] (cRGD) peptide units on DNA origami were employed. The incorporation of disulfide bonds allowed the release of multiple modules in response to intracellular glutathione (GSH) in tumors. The nanodevice promoted the infiltration of CD8+ and CD4+ cells into the tumor and generated a highly inflamed TME, thereby enhancing the effectiveness of cancer immunotherapy. Our research results indicate that the nanodevice we constructed can effectively inhibit tumor growth and prevent lung metastasis without obvious systemic toxicity, providing a promising strategy for cancer combination treatment. [ABSTRACT FROM AUTHOR]

Background: Among mechanoporation techniques for intracellular delivery, microfluidic approaches succeed in high delivery efficiency and throughput. However, especially the entry of large cargoes (e.g. DNA origami, mRNAs, organic/inorganic nanoparticles) is currently impaired since it requires large cell membrane pores with the need to apply multi-step processes and high forces, dramatically reducing cell viability. Results: Here, HiViPore presents as a microfluidic viscoelastic contactless compression for one-step cell mechanoporation to produce large pores while preserving high cell viability. Inducing an increase of curvature at the equatorial region of cells, formation of a pore with a size of ~ 1 μm is obtained. The poration is coupled to an increase of membrane tension, measured as a raised fluorescence lifetime of 12% of a planarizable push-pull fluorescent probe (Flipper-TR) labelling the cell plasma membrane. Importantly, the local disruptions of cell membrane are transient and non-invasive, with a complete recovery of cell integrity and functions in ~ 10 min. As result, HiViPore guarantees cell viability as high as ~ 90%. In such conditions, an endocytic-free diffusion of large nanoparticles is obtained with typical size up to 500 nm and with a delivery efficiency up to 12 times higher than not-treated cells. Conclusions: The proposed one-step contactless mechanoporation results in an efficient and safe approach for advancing intracellular delivery strategies. In detail, HiViPore solves the issues of low cell viability when multiple steps of poration are required to obtain large pores across the cell plasma membrane. Moreover, the compression uses a versatile, low-cost, biocompatible viscoelastic fluid, thus also optimizing the operational costs. With HiViPore, we aim to propose an easy-to-use microfluidic device to a wide range of users, involved in biomedical research, imaging techniques and nanotechnology for intracellular delivery applications in cell engineering. [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]

Current in vitro models struggle to balance the complexity of human diseases with suitability for large-scale drug tests. While 3D cultures simulate human tissues, they lack cellular intricacy, and integrating these models with high-throughput drug screening remains a challenge. Here, we introduce a method that uses self-assembling nucleic acid nanostructures decorated living cells, termed NACs, to create spheroids with a customizable 3D layout. To demonstrate its uniqueness, our method effectively creates designer 3D spheroids by combining parenchymal cells, stromal cells, and immune cells, leading to heightened physiological relevance and detailed modeling of complex chronic diseases and immune-stromal interactions. Our approach achieves a high level of biological fidelity while being standardized and straightforward to construct with the potential for large-scale drug discovery applications. By merging the precision of DNA nanotechnology with advanced cell culture techniques, we are streamlining human-centric models, striking a balance between complexity and standardization, to boost drug screening efficiency. [ABSTRACT FROM AUTHOR]

Stimuli‐responsive patterned photonic actuators, characterized by their patterned nano/microscale structures and capacity to demonstrate synergistic color changes and shape morphing in response to external stimuli, have attracted intense scientific attention. However, traditional patterned photonic actuator systems still face limitations such as cumbersome and time‐consuming preparation processes and small‐scale deformations. Herein, we introduce a facile approach involving an athermal embossing technique to rapidly fabricate patterned photonic actuators based on near‐infrared (NIR) light‐responsive liquid crystal elastomers. The resulting patterned photonic actuators demonstrate remarkable features, including brilliant angle‐dependent structural color, complex three‐dimensional actuation, and good color durability under NIR light stimulation. As illustrative demonstrations of the proof‐of‐concept, we fabricate two light‐fuelled patterned photonic soft actuators: a butterfly‐inspired actuator that can produce wing‐flapping dynamic changes in structural color, and an origami crane‐shaped actuator with shape memory, structural color information storage, and dynamic display properties. This strategy provides distinct insights into the design and fabrication of various patterned photonic soft robotic devices and intelligent actuators. [ABSTRACT FROM AUTHOR]

Cells switch genes ON or OFF by altering the state of chromatin via histone modifications at specific regulatory locations along the chromatin polymer. These gene regulation processes are carried out by a network of reactions in which the histone marks spread to neighboring regions with the help of enzymes. In the literature, this spreading has been studied as a purely kinetic, non-diffusive process considering the interactions between neighboring nucleosomes. In this work, we go beyond this framework and study the spreading of modifications using a reaction-diffusion (RD) model accounting for the diffusion of the constituents. We quantitatively segregate the modification profiles generated from kinetic and RD models. The diffusion and degradation of enzymes set a natural length scale for limiting the domain size of modification spreading, and the resulting enzyme limitation is inherent in our model. We also demonstrate the emergence of confined modification domains without the explicit requirement of a nucleation site. We explore polymer compaction effects on spreading and show that single-cell domains may differ from averaged profiles. We find that the modification profiles from our model are comparable with existing H3K9me3 data of S. pombe. Author summary: DNA is folded into chromatin by wrapping it around histone protein octamers, forming a string of nucleosome beads. The chemical modifications on histone proteins along the one-dimensional string form a significant part of the epigenetic code. This code determines whether a chromatin region is likely to be active or repressed. How the chemical modification patterns arise, and their stability along the histone proteins is a question of great interest. While some players in this process are known, how the physical process of diffusion and reaction of the enzymes collectively dictate the pattern formation is unknown. In this work, we simulate histone modification spreading accounting for explicit diffusion and reaction of the essential constituents. We show that the diffusion and degradation processes of the constituents limit the size of the modification domain. We also show how the availability of enzymes and the compaction of the chromatin affect the spreading of the histone modification. [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 adhesion of circulating tumor cells (CTCs) to the endothelial lumen and their extravasation to surrounding tissues are crucial in the seeding of metastases and remain the most complex events of the metastatic cascade to study. Integrins expressed on CTCs are major regulators of the extravasation process. This knowledge is primarily derived from animal models and biomimetic systems based on artificial endothelial layers, but these methods have ethical or technical limitations. We present a versatile microfluidic device to study cancer cell extravasation that mimics the endothelial barrier by using a porous membrane functionalized with DNA origami nanostructures (DONs) that display nanoscale patterns of adhesion peptides to circulating cancer cells. The device simulates physiological flow conditions and allows direct visualization of cell transmigration through microchannel pores using 3D confocal imaging. Using this system, we studied integrin‐specific adhesion in the absence of other adhesive events. Specifically, we show that the transmigration ability of the metastatic cancer cell line MDA‐MB‐231 is influenced by the type, distance, and density of adhesion peptides present on the DONs. Furthermore, studies with mixed ligand systems indicate that integrins binding to RGD (arginine‐glycine‐aspartic acid) and IDS (isoleucine‐aspartic acid‐serine) did not synergistically enhance the extravasation process of MDA‐MB‐231 cells. [ABSTRACT FROM AUTHOR]

DNA origami nanostructures (DOs) are promising tools for applications including drug delivery, biosensing, detecting biomolecules, and probing chromatin substructures. Targeting these nanodevices to mammalian cell nuclei could provide impactful approaches for probing, visualizing, and controlling biomolecular processes within live cells. We present an approach to deliver DOs into live-cell nuclei. We show that these DOs do not undergo detectable structural degradation in cell culture media or cell extracts for 24 hours. To deliver DOs into the nuclei of human U2OS cells, we conjugated 30-nanometer DO nanorods with an antibody raised against a nuclear factor, specifically the largest subunit of RNA polymerase II (Pol II). We find that DOs remain structurally intact in cells for 24 hours, including inside the nucleus. We demonstrate that electroporated anti-Pol II antibody-conjugated DOs are piggybacked into nuclei and exhibit subdiffusive motion inside the nucleus. Our results establish interfacing DOs with a nuclear factor as an effective method to deliver nanodevices into live-cell nuclei. [ABSTRACT FROM AUTHOR]

Topological indices quantify the connectivity and structural properties of chemical compounds. We use the topological indices for predicting and evaluating the numerous properties of molecules, such as boiling temperatures, toxicity, and biological activity. Zagreb connection indices are a useful tool for studying the structural characteristics of the DNA backbone network. These indices provide important information on the arrangement and connections between nucleotide bases inside the DNA molecule. These indices show compactness, complexity, and topological properties in order to predict DNA bending propensity, DNA-protein interaction, and DNA stability. DNA folding patterns and the impact of mutations on DNA networks are areas of further research for these topological indices. In this study, we calculate Zagreb connection indices and modified Zagreb connection indices for backbone DNA network and subdivided backbone DNA network. Furthermore, we compute the hyper-Zagreb connection index, the inverse sum connection index, and the harmonic connection index. [ABSTRACT FROM AUTHOR]

The incorporation of histone variants has structural ramifications on nucleosome dynamics and stability. Due to their unique sequences, histone variants can alter histone–histone or histone–DNA interactions, impacting the folding of DNA around the histone octamer and the overall higher-order structure of chromatin fibers. These structural modifications alter chromatin compaction and accessibility of DNA by transcription factors and other regulatory proteins to influence gene regulatory processes such as DNA damage and repair, as well as transcriptional activation or repression. Histone variants can also generate a unique interactome composed of histone chaperones and chromatin remodeling complexes. Any of these perturbations can contribute to cellular plasticity and the progression of human diseases. Here, we focus on a frequently overlooked group of histone variants lying within the four human histone gene clusters and their contribution to breast cancer. [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]

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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]

The coupling of structural transitions to heat capacity changes leads to destabilization of macromolecules at both elevated and lowered temperatures. DNA origami not only exhibit this property but also provide a nanoscopic observable of cold denaturation processes by directing intramolecular strain to the most sensitive elements within their hierarchical architecture. [ABSTRACT FROM AUTHOR]

The document is a contents list for the journal Chemical Communications, published by The Royal Society of Chemistry. It includes a feature article on the use of tetrazoles in constructing assemblies, as well as several communications on various topics such as electron-poor Au(III) trication, cold denaturation of DNA origami nanostructures, and optical discrimination of terpenes in citrus peels. The journal aims to connect the global chemistry community and publishes work from scientists at all career stages and countries. [Extracted from the article]

Molecular computing is an emerging paradigm that plays an essential role in data storage, bio-computation, and clinical diagnosis with the future trends of more efficient computing scheme, higher modularity with scaled-up circuity and stronger tolerance of corrupted inputs in a complex environment. Towards these goals, we construct a spatially localized, DNA integrated circuits-based classifier (DNA IC-CLA) that can perform neuromorphic architecture-based computation at a molecular level for medical diagnosis. The DNA-based classifier employs a two-dimensional DNA origami as the framework and localized processing modules as the in-frame computing core to execute arithmetic operations (e.g. multiplication, addition, subtraction) for efficient linear classification of complex patterns of miRNA inputs. We demonstrate that the DNA IC-CLA enables accurate cancer diagnosis in a faster (about 3 h) and more effective manner in synthetic and clinical samples compared to those of the traditional freely diffusible DNA circuits. We believe that this all-in-one DNA-based classifier can exhibit more applications in biocomputing in cells and medical diagnostics. Molecular computing is an emerging paradigm with a crucial role in clinical diagnosis. Here, authors develop a spatially localized, DNA-integrated circuits-based classifier, DNA IC-CLA, which enables accurate cancer diagnosis for clinical samples in a faster and more effective manner. [ABSTRACT FROM AUTHOR]

Transmembrane proteins transmit chemical signals as well as mechanical cues. The latter is often achieved by coupling to the cytoskeleton. The incorporation of fully engineerable membrane‐spanning structures for the transduction of chemical and, in particular, mechanical signals is therefore a critical aim for bottom‐up synthetic biology. Here, a membrane‐spanning DNA origami signaling units (DOSUs) is designed and mechanically coupled to DNA cytoskeletons encapsulated within giant unilamellar vesicles (GUVs). The incorporation of the DOSUs into the GUV membranes is verified and clustering upon external stimulation is achieved. Dye‐influx assays reveal that clustering increases the insertion efficiency. The transmembrane‐spanning DOSUs act as pores to allow for the transport of single‐stranded DNA into the GUVs. This is employed to trigger the reconfiguration of DNA cytoskeletons within GUVs. In addition to chemical signaling, mechanical coupling of the DOSUs to the internal DNA cytoskeletons is induced. With chemical cues from the environment, clustering of the DOSUs is induced, which triggers a symmetry break in the organization of the DNA cytoskeleton inside of the GUV. DNA‐based transmembrane structures are engineered that transduce signals without transporting the signaling molecule itself—providing a route toward signal processing and adaptive synthetic cells. [ABSTRACT FROM AUTHOR]

Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility of self-assembling complex lattices or finite-size constructs. However, attempts so far have mostly only been successful in silico and often fail in experiment because of unpredicted traps associated with kinetic slowing down (gelation, glass transition) and competing ordered structures. Theoretical predictions also face the difficulty of encoding the desired interparticle interaction potential with the experimentally available nano- and micrometer-sized particles. To overcome these issues, we combine SAT assembly (a patchy-particle interaction design algorithm based on constrained optimization) with coarse-grained simulations of DNA nanotechnology to experimentally realize trap-free self-assembly pathways. We use this approach to assemble a pyrochlore three-dimensional lattice, coveted for its promise in the construction of optical metamaterials, and characterize it with small-angle x-ray scattering and scanning electron microscopy visualization. [ABSTRACT FROM AUTHOR]

Colloidal self-assembly allows rational design of structures on the micrometer and submicrometer scale. One architecture that can generate complete three-dimensional photonic bandgaps is the diamond cubic lattice, which has remained difficult to realize at length scales comparable with the wavelength of visible or ultraviolet light. In this work, we demonstrate three-dimensional photonic crystals self-assembled from DNA origami that act as precisely programmable patchy colloids. Our DNA-based nanoscale tetrapods crystallize into a rod-connected diamond cubic lattice with a periodicity of 170 nanometers. This structure serves as a scaffold for atomic-layer deposition of high-refractive index materials such as titanium dioxide, yielding a tunable photonic bandgap in the near-ultraviolet. [ABSTRACT FROM AUTHOR]

Introduction: DNA barcoding in insects has progressed rapidly, with the ultimate goal of a complete inventory of the world's species. However, the barcoding effort to date has been driven by a few national campaigns and leaves much of the world unsampled. This study investigates to what degree the current barcode data cover the species diversity across the globe, using the leaf beetle family Chrysomelidae as an example. Methods: A recent version (June 2023) of the Barcode-of-Life database was subjected to test of sampling completeness using the barcode-to-BIN ratio and sampling coverage (SC) metric. All barcodes were placed in a phylogenetic tree of ~600 mitochondrial genomes, applying phylogenetic diversity (PD) and metrics of community phylogenetics to national barcode sets to test for sampling completeness at clade level and reveal the global structure of species diversity. Results: The database included 73342 barcodes, grouped into 5310 BINs (species proxies) from 101 countries. Costa Rica contributed nearly half of all barcode sequences, while nearly 50 countries were represented by less than ten barcodes. Only five countries, Costa Rica, Canada, South Africa, Germany, and Spain, had a high sampling completeness, although collectively the barcode database covers most major taxonomic and biogeographically confined lineages. PD showed moderate saturation as more species diversity is added in a country, and community phylogenetics indicated clustering of national faunas. However, at the species level the inventory remained incomplete even in the most intensely sampled countries, and the sampling was insufficient for assessment of global species richness patterns. Discussion: The sequence-based inventory in Chrysomelidae needs to be greatly expanded to include more areas and deeper local sampling before reaching a knowledge base similar to the existing Linnaean taxonomy. However, placing the barcodes into a backbone phylogenetic tree from mitochondrial genomes, a taxonomically and biogeographically highly structured pattern of global diversity emerges into which all species can be integrated via their barcodes. [ABSTRACT FROM AUTHOR]