A DNA-based method for rationally assembling nanoparticles into macroscopic materials

Remodeling of Effector and Regulatory T Cells by Capture and Utilization of miRNAs Using Nanocomposite Hydrogel for Tumor-Specific Photothermal Immunotherapy

In immunotherapy for malignant tumors, the dysregulation of the balance between effector T cells and regulatory T cells (Tregs) and the uncertain efficacy due to individual differences have been considered as two critical challenges. In this study, we engineered an injectable nanocomposite hydrogel system (SNAs@M-Gel) capable of suppressing Treg proliferation and blocking PD-1/PD-L1-mediated immune evasion effectively, achieved through the stimulus-responsive modulation of multiple tumor-associated microRNAs. Simultaneously, this system enables microRNA-dependent photothermal immunotherapy, facilitating a highly efficient and personalized approach to tumor treatment. Specifically, oxidized sodium alginate (OSA) and cancer cell membrane (CCM)-encapsulated spherical nucleic acid nanoparticles (SNAs@M) were used to construct the SNAs@M-Gel hydrogel in situ at the tumor site through the formation of pH-sensitive Schiff base bonding and cross-linking using endogenous calcium ions (Ca2+). During treatment, SNAs@M-Gel was retained locally for up to 10 days, and SNAs@M nanoparticles were continuously released into the tumor microenvironment. Through the targeting ability of CCM, SNAs@M precisely entered tumor cells and specifically hybridized with the overexpressed miR-214 and miR-130a, leading to a significant downregulation of PD-L1 expression on tumor cells and the restoration of cytotoxic T lymphocyte (CTL) function suppressed by Tregs, thereby remodeling the immune microenvironment. In addition, miRNAs functioned as cross-linking agents, facilitating the aggregation of SNAs and allowing the localized production of photothermal agents directly inside tumor cells, which, under near-infrared (NIR) irradiation, promoted highly selective photothermal therapy. This cascade of events not only led to the destruction of the primary tumor but also resulted in the release of a substantial number of tumor-related antigens, which triggered the maturation of adjacent dendritic cells (DCs) and subsequent priming of tumor-specific CTLs, while simultaneously depleting Tregs, thereby reversing the tumor-promoting immune microenvironment and enhancing the overall therapeutic efficacy of photothermal immunotherapy.

Effect of Surface Modification of Gold Nanoparticles Loaded with Small Nucleic Acid Sequences on Cytotoxicity and Uptake: A Comparative Study In Vitro

Nanoparticle technology, particularly gold nanoparticles (AuNPs), is being developed for a wide range of applications, including as a delivery system of peptides or nucleic acids (NA). Their use in precision medicine requires detailed engineering of NP functionalization to optimize their function and minimize off-target toxicity. Two main routes can be found in the literature for the attachment of NA strands to AuNPs: covalent binding via a thiol group or passive adsorption onto a specially adapted coating previously applied to the metallic core. In this latter case, the coating is often a positively charged polymer, as polyethylenimine, which due to its high positive charge can induce cytotoxicity. Here, we investigated an innovative strategy based on the initial coating of the particles using calix[4]arene macrocycles bearing polyethylene glycol chains as an interesting alternative to polyethylenimine for NA adsorption. Because any molecular modification of AuNPs may affect the cytotoxicity and cellular uptake, we compared the behavior of these AuNPs to that of particles obtained via a classical thiol covalent attachment in MCF-7 and GC-1 spg cell lines. We showed a high biocompatibility of both AuNPs-NA internalized in vitro. The difference in subcellular localization of both AuNPs-NA in MCF-7 cells compared to GC-1 spg cells suggests that their subcellular target is cell- and coating-dependent. This finding provides valuable insights for developing alternative NA delivery systems with a high degree of tunability.

Cocrystals combining order and correlated disorder via colloidal crystal engineering with DNA

Colloidal cocrystallization enables the formation of multicomponent materials with unique physicochemical properties, yet the role of nanoparticle (NP) shape and specific ligand interactions to cocrystallize anisotropic and isotropic NPs, with order and correlated disorder, remains underexplored. Here, geometry-inspired strategies along with programmable DNA interactions are combined to achieve structural control of colloidal cocrystal assemblies. Coassembling polyhedral and spherical NPs with complementary DNA yields two classes of cocrystals: one where both components order, and another where polyhedral NPs form a periodic lattice, while spherical NPs remain disordered but spatially correlated with polyhedral edges and corners. The size ratio of the building blocks can be used to control the ordering of spherical NPs-smaller octahedral-to-sphere size ratios favor fully ordered cocrystals. Molecular dynamics simulations further elucidate the role of NP shapes and dimensions in the structural outcome of the cocrystal. This work provides a framework for deliberately targeting and accessing crystals with exotic multicomponent structures.

Convergence of DNA nanotechnology and polymer chemistry to 'synthesize' nanopolymers with branching architectures: a computational perspective

Polymer-like superstructures termed nanopolymers from the self-assembly of atom-like nanoparticles are an emerging class of structured metamaterials with enhanced functionalities, but the controllable 'synthesis' of nanopolymers with non-linear architecture and spatially defined dimensions remains a challenge. Inspired by synthetic concepts of branched polymers, we propose a hierarchical polymerization-like protocol for the programmable coassembly of DNA-based multicomponent mixtures into non-linear nanopolymers with well-defined branching architecture and predictable spatial dimensions. By employing computational simulations, it is theoretically demonstrated that the synergy of sequence-designed DNA motifs and the proposed protocol enables the precise control over the assembly kinetics of atom-like nanoparticles and the branching architectures of nanopolymers, in agreement with the predictions of the generalized polymerization kinetics model. Furthermore, it is demonstrated that the fundamental correlations between the spatial dimension and branching architecture of nanopolymers satisfy the scaling law acquired in polymer science. These findings will facilitate the programmable coassembly of DNA supramolecules into structured metamaterials with architectural complexity observed in nature.

Core-Shell Microgels at Air/Water Interfaces: Role of Interfacial Tension in Monolayer Evolution

Core-shell microgels with rigid cores and soft, deformable hydrogel shells can assemble at air-water interfaces, forming freely floating monolayers. The strong adsorption at such interfaces is related to the reduction in interfacial tension, which also causes the microgels to deform laterally. The degree of this deformation is typically controlled through applied surface pressure. Until now, surprisingly little has been known about the impact of interfacial tension imbalances between interfacial areas covered with a microgel monolayer and microgel-free areas in the surroundings. In this work, we systematically study the monolayer evolution at air/water interfaces in dependence of interfacial tension controlled by the addition of sodium dodecyl sulfate or linear poly-N-isopropylacrylamide homopolymer to the free area. We do this by globally monitoring the evolution of the area of freely floating monolayers. Macroscopic changes are also related to the local microstructure studied by atomic force microscopy (AFM). Depending on the interfacial tension imbalance, the monolayer either expands, shrinks, or maintains its conformation. The kinetics of monolayer expansion is compared for core-shell microgels with the same silica core and varying cross-linker densities. Our study reveals the impact of interfacial tension on the behavior of microgel monolayers at liquid interfaces and also provides useful insights into controlling the two-dimensional (2D) microstructure without the need for a Langmuir trough.

Understanding the Growth Mechanism of Thiol-Conjugated Au25 Cluster

The synthesis of ligand-conjugated gold nanoclusters has attracted significant attention due to its ability to achieve precise control over cluster size selectivity. Among these, Au25(SR)18 -, where R represents an alkyl group, is one of the earliest being synthesized with a very high yield, although its growth mechanism is yet to be fully understood. Using density functional theory, we present the results of a theoretical investigation on the growth process of Au25(SR)18 -, beginning from Au13(SR)12 -. Our findings indicate that the sulfur atoms in the core structure of Au13(SR)12 - preferentially bond with Au-thiol monomers. Monomers attached to two adjacent triangular faces form a staple motif of the gold-sulfur chain, releasing a single linear thiol radical. These reactions occur along the six mutually perpendicular ridges of the Au13 core. The remaining eight triangular faces, linked with linear alkyl parts, cannot bind additional Au-thiol monomers, stopping cluster growth. Furthermore, the capping gold-sulfur chains play a protective role for the core, facilitating the stable formation of the Au25(SR)18 -cluster, as confirmed experimentally.

Concept and Development of Metal-Framework Nucleic Acids

Based on the Watson-Crick base pairing principle, precisely programmable metal-framework nucleic acids (mFNA) have evolved from one-dimensional to three-dimensional nanoscale structures, a technological advancement attributed to progress in DNA nanotechnology. mFNA are a new type of nanomaterial formed by using framework nucleic acids (FNAs) as precise templates to guide the ordered assembly and self-assembly of metal ions, metal salts (such as calcium phosphate, calcium carbonate, etc.), metal nanoclusters, metal nanoparticles, or metal oxide nanoparticles. Compared to traditional FNAs, mFNA not only inherits the powerful programmed self-assembly capabilities of nucleic acids but also incorporates the unique physicochemical properties of inorganic metal nanomaterials. This intersection of organic and inorganic chemistry presents broad application prospects in fields such as biology, chemistry, materials science, and energy science. This review, based on the principles related to FNAs, introduces the concept of mFNA for the first time, aiming to explore the fundamental connections between nanoscale FNAs and metal materials. Additionally, the article focuses on the construction methods and functional characteristics of mFNA. Finally, the current challenges faced by mFNA are reviewed, and their future development is anticipated, providing detailed information for a comprehensive understanding of the research progress in mFNA.

Nanofabrication for Nanophotonics

Nanofabrication, a pivotal technology at the intersection of nanoscale engineering and high-resolution patterning, has substantially advanced over recent decades. This technology enables the creation of nanopatterns on substrates crucial for developing nanophotonic devices and other applications in diverse fields including electronics and biosciences. Here, this mega-review comprehensively explores various facets of nanofabrication focusing on its application in nanophotonics. It delves into high-resolution techniques like focused ion beam and electron beam lithography, methods for 3D complex structure fabrication, scalable manufacturing approaches, and material compatibility considerations. Special attention is given to emerging trends such as the utilization of two-photon lithography for 3D structures and advanced materials like phase change substances and 2D materials with excitonic properties. By highlighting these advancements, the review aims to provide insights into the ongoing evolution of nanofabrication, encouraging further research and application in creating functional nanostructures. This work encapsulates critical developments and future perspectives, offering a detailed narrative on the state-of-the-art in nanofabrication tailored for both new researchers and seasoned experts in the field.

Sulfate-reducing bacteria in removal of pollutants: a promising candidate for bioremediation

Industrial processes contribute significantly to environmental pollution, particularly by releasing sulfate-rich wastewater containing toxic metals and organic pollutants. Sulfate-reducing bacteria (SRB), being anaerobic microorganisms, are capable of reducing sulfate to sulfide, which precipitates harmful heavy metals and facilitates bioremediation. This review explores the potential of SRB in industrial wastewater treatment, focusing on their roles in the bioremediation of sulfates, heavy metals, and persistent organic pollutants (POPs). Laboratory-scale experiments demonstrated that SRB effectively reduces sulfate concentrations and removes heavy metals such as zinc, cadmium, and chromium through sulfidogenesis. The treatment process shows promise as an eco-friendly alternative to conventional chemical methods. However, challenges related to hydrogen sulfide emissions and process scalability persist. Future research focuses on enhancing SRB activity through optimized bioreactor designs while effectively controlling H2S release. This review emphasizes SRB as a promising candidate for industrial applications in wastewater treatment and environmental management.

The underappreciated role of nonspecific interactions in the crystallization of DNA-coated colloids

Over the last decade, the field of programmable self-assembly has seen an explosion in the diversity of crystal lattices that can be synthesized from DNA-coated colloidal nanometer- and micrometer-scale particles. The prevailing wisdom has been that a particular crystal structure can be targeted by designing the DNA-mediated interactions, to enforce binding between specific particle pairs, and the particle diameters, to control the packing of the various species. In this article, we show that other ubiquitous nonspecific interactions can play equally important roles in determining the relative stability of different crystal polymorphs and therefore what crystal structure is most likely to form in an experiment. For a binary mixture of same-sized DNA-coated colloidal micrometer-scale particles, we show how changing the magnitudes of nonspecific steric and van der Waals interactions gives rise to a family of binary body-centered tetragonal crystals, including both cesium-chloride and copper-gold crystals. Simulations using pair potentials that account for these interactions reproduce our experimental observations quantitatively, and a theoretical model reveals how a subtle balance between specific and nonspecific forces determines the equilibrium crystal structure. These results highlight the importance of accounting for nonspecific interactions in the crystal-engineering design process.

OligoA-tailed DNA for dense functionalization of gold nanoparticles and nanorods in minutes without thiol-modification: unlocking cross-disciplinary applications

DNA-functionalized gold nanoparticles (DNA-AuNPs) and nanorods (DNA-AuNRs) have emerged as key yet versatile biomaterials for applications in biosensing, diagnostics and programmable assembly. The high cost and sometimes complex procedures of functionalization of DNA onto AuNPs and AuNRs via the Au-thiol interaction may have set a threshold for its expanded application by researchers of diverse fields. Although oligoA-tailed DNA has been introduced as an alternative to thiolated DNA, its extended use has been largely confined to spherical nanoparticles with suboptimal functionalization density. Here we show a rapid and efficient method for high-density functionalization of both AuNPs and AuNRs using oligoA-tailed DNA via butanol dehydration, with the length of oligoA as short as A2. By preventing secondary structure formation at an elevated temperature, our results demonstrate significantly enhanced DNA adsorption, further allowing for functionalization of a random sequence onto the AuNPs. This yields stable DNA-nanoparticle conjugates with superior stability and durability, suitable for in situ naked-eye loop-mediated isothermal amplification (LAMP) assay of bacterial pathogens and stimuli-responsive self-assembly. This study overcomes long-standing barriers in rapid, simple and low-cost preparation of DNA-AuNPs and DNA-AuNRs, paving the way for cross-disciplinary applications in diverse fields that were previously siloed and beyond.

Chiroptical hybrid nanomaterials based on metal nanoparticles and biomolecules

Chirality at the nanoscale has recently attracted renewed attention from the scientific community. As a result, various strategies have been proposed to develop chiral nanomaterials based on metal nanoparticles and chiral biomolecules such as DNA, amino acids, or proteins. We review herein the past and recent literature related to the functionalization of metal nanoparticles with various chiral biomolecules and their assembly into biomaterials with chiroptical response. We divide the review into two main parts, according to the class of biomolecules. We first discuss mechanisms employed to obtain chiral bioconjugates based on metal nanoparticles and amino acids or their derivatives (peptides and proteins), including mechanisms for chirality transfer from chiral biomolecules to achiral nanoparticles. We also review the use of amino acids/peptides as either chiral inducers for the growth of chiral nanoparticles or templates for the chiral arrangement of achiral nanoparticles. In the second part we present an overview of methods to prepare bioconjugates comprising DNA and metal nanoparticles, as well as selected examples of helical nanoparticle arrangements that employ DNA as a chiral template.

Recent advances in nucleic acid-functionalized metallic nanoparticles

Nucleic acid-functionalized metallic nanoparticles (N-MNPs) precisely integrate the advantageous characteristics of nucleic acids and metallic nanomaterials, offering various abilities such as resistance to enzymatic degradation, penetration of physiological barriers, controllable mobility, biomolecular recognition, programmable self-assembly, and dynamic structure-function transformation. These properties demonstrate significant potential in the field of biomedical diagnostics and therapeutics. In this review, we examine recent advancements in the construction and theranostic applications of N-MNPs. We briefly summarize the methodologies employed in the conjugation of nucleic acids with metallic nanoparticles and the formation of their superstructural assemblies. We highlight recent representative applications of N-MNPs in biomolecular diagnosis, imaging, and smart delivery of theranostic agents. We also discuss challenges currently faced in this field and provide an outlook on future development directions and application prospects.

Transfection via RNA-Based Nanoparticles: Comparing Encapsulation vs Adsorption Approaches of RNA Incorporation

Historically, RNA delivery via nanoparticles has primarily relied on encapsulation, as demonstrated by lipid nanoparticles in SARS-CoV-2 vaccines. Concerns about RNA degradation on nanoparticle surfaces initially limited the exploration of adsorption-based approaches. However, recent advancements have renewed interest in adsorption as a viable alternative. This Viewpoint explores the approaches of RNA incorporation in nanoparticles, comparing encapsulation, adsorption, and the combination of encapsulation and adsorption, and presents a framework to guide the selection of the most suitable strategy based on general characteristics.

DNA‑Directed Assembly of Photonic Nanomaterials for Diagnostic and Therapeutic Applications

DNA-directed assembly has emerged as a versatile and powerful approach for constructing complex structured materials. By leveraging the programmability of DNA nanotechnology, highly organized photonic systems can be developed to optimize light-matter interactions for improved diagnostics and therapeutic outcomes. These systems enable precise spatial arrangement of photonic components, minimizing material usage, and simplifying fabrication processes. DNA nanostructures, such as DNA origami, provide a robust platform for building multifunctional photonic devices with tailored optical properties. This review highlights recent progress in DNA-directed assembly of photonic nanomaterials, focusing on their applications in diagnostics and therapeutics. It provides an overview of the latest advancements in the field, discussing the principles of DNA-directed assembly, strategies for functionalizing photonic building blocks, innovations in assembly design, and the resulting optical effects that drive these developments. The review also explores how these photonic architectures contribute to diagnostic and therapeutic applications, emphasizing their potential to create efficient and effective photonic systems tailored to specific healthcare needs.

Chondroitin Sulfate-Coated Heteroduplex-Molecular Spherical Nucleic Acids

Molecular Spherical Nucleic Acids (MSNAs) are atomically uniform dendritic nanostructures and potential delivery vehicles for oligonucleotides. The radial formulation combined with covalent conjugation may hide the oligonucleotide content and simultaneously enhance the role of appropriate conjugate groups on the outer sphere. The conjugate halo may be modulated to affect the delivery properties of the MSNAs. In the present study, [60]fullerene-based molecular spherical nucleic acids, consisting of a 2'-deoxyribonucleotide and a ribonucleotide sequence, were used as hybridization-mediated carriers ("DNA and RNA-carriers") for an antisense oligonucleotide, suppressing Tau protein, (i. e. Tau-ASO) and its conjugates with chondroitin sulfate tetrasaccharides (CS) with different sulfation patterns. The impact of the MSNA carriers, CS-moieties on the conjugates and the CS-decorations on the MSNAs on cellular uptake and - activity (Tau-suppression) of the Tau-ASO was studied with hippocampal neurons in vitro. The formation and stability of these heteroduplex ASO-MSNAs were evaluated by UV melting profile analysis, polyacrylamide gel electrophoresis (PAGE), dynamic light scattering (DLS) and size exclusion chromatography equipped with a multi angle light scattering detector (SEC-MALS). The cellular uptake and - activity were studied by confocal microscopy and Western blot analysis, respectively.

Nanostar self-assemblies of spherical nanoparticles inside lipid vesicles

Curvature deformations of lipid membranes resulting from the adhesion of nanoparticles (NPs) often lead to effective interactions between the NPs, resulting in their self-assembly. Many studies have shown that this interaction is attractive in the case of NPs with uniform surfaces adhering to the outer leaflet of lipid vesicles. This interaction leads to the NPs' self-assembly into in-plane or out-of-plane linear chains in which they are uni-dimensionally close-packed. In this article, we show, through coarse-grained molecular dynamics simulations, that spherical NPs with uniform surfaces adhering to the inner leaflet of lipid vesicles experience repulsive interactions, resulting in NP configurations in which they are apart. Systematic simulation sets with respect to the number of NPs inside vesicles and the strength of their adhesion to the membrane show an interesting phase diagram with different adhesion modes. These include a three-dimensional clustering mode, which is fairly dynamic at low adhesion strength and rigid at moderately high adhesion strength. These two regimes are separated by an intriguing two-dimensional clustering mode at moderate values of the adhesion strength. In this mode, the NPs form ordered planar nanostars with geometries determined by the number of NPs. In contrast to the three-dimensional mode, in the two-dimensional clustering mode, the NPs are anisotropically wrapped by the NPs with the largest degree of wrapping along the plane normal to the nanostar plane and the lowest degree of wrapping along the plane of the nanostar.

Models and simulations of structural DNA nanotechnology reveal fundamental principles of self-assembly

DNA is not only a centrally important molecule in biology: the specificity of bonding that allows it to be the primary information storage medium for life has also allowed it to become one of the most promising materials for designing intricate, self-assembling structures at the nanoscale. While the applications of these structures are both broad and highly promising, the self-assembly process itself has attracted interest not only for the practical applications of designing structures with more efficient assembly pathways, but also due to a desire to understand the principles underlying self-assembling systems more generally, of which DNA-based systems provide intriguing and unique examples. Here, we review the fundamental physical principles that underpin the self-assembly process in the field of DNA nanotechnology, with a specific focus on simulation and modelling and what we can learn from them. In particular, we compare and contrast DNA origami and bricks and briefly outline other approaches, with an overview of concepts such as cooperativity, nucleation and hysteresis; we also explain how nucleation barriers can be controlled and why they can be helpful in ensuring error-free assembly. While high-resolution models may be needed to obtain accurate system-specific properties, often very simple coarse-grained models are sufficient to extract the fundamentals of the underlying physics and can enable us to gain deep insight. By combining experimental and simulation approaches to understand the details of the self-assembly process, we can optimise its yields and fidelity, which may in turn facilitate its use in practical applications.

Applications of DNA functionalized gold nanozymes in biosensing

In recent years, nanozymes have emerged as highly potential substitutes, surpassing the performance of natural enzymes. Among them, gold nanoparticles (AuNPs) and their metal hybrids have become a hot topic in nanozyme research due to their facile synthesis, easy surface modification, high stability, and excellent enzymatic activity. The integration of DNA with AuNPs, by precisely controlling the assembly, arrangement, and functionalization of nanoparticles, greatly facilitates the development of highly sensitive and selective biosensors. This review comprehensively elaborates on three core strategies for the combination of DNA with AuNPs, and deeply analyzes two widely applied enzyme activities in the field of sensing technology and the catalytic principles behind them. On this basis, we systematically summarize various methods for regulating the activity of gold nanozymes by DNA. Following that, we comprehensively review the latest research trends of DNA-Au nanozymes in the field of biosensing, with a particular focus on several crucial application areas such as food safety, environmental monitoring, and disease diagnosis. In the conclusion of the article, we not only discuss the main challenges faced in current research but also look forward to potential future research directions.

Single Nucleotide Polymorphism Highlighted via Heterogeneous Light-Induced Dissipative Structure

The unique characteristics of biological structures depend on the behavior of DNA sequences confined in a microscale cell under environmental fluctuations and dissipation. Here, we report a prominent difference in fluorescence from dye-modified single-stranded DNA in a light-induced assembly of DNA-functionalized heterogeneous probe particles in a microwell of several microliters in volume. Strong optical forces from the Mie scattering of microparticles accelerated hybridization, and the photothermal effect from the localized surface plasmons in gold nanoparticles enhanced specificity to reduce the fluorescence intensity of dye-modified DNA to a few %, even in a one-base mismatched sequence, enabling us to clearly highlight the single nucleotide polymorphisms in DNA. Fluorescence intensity was positively correlated with complementary DNA concentrations ranging in several tens fg/μL after only 5 min of laser irradiation. Remarkably, a total amount of DNA in an optically assembled structure of heterogeneous probe particles was estimated between 2.36 ymol (2.36 × 10-24 mol) and 2.36 amol (2.36 × 10-18 mol) in the observed concentration range. These findings can promote an innovative production method of nanocomposite structures via biological molecules and biological sensing with simple strategies avoiding genetic amplification in a PCR-free manner.

Spherical Nucleic Acids Meet Acoustic Levitation: A Breakthrough in Synthesis and Application

Spherical nucleic acids (SNAs), with their densely packed nucleic acid shells and programmable functionalities, have become indispensable in nanomedicine and biosensing. Developed synthesis methods, including salt aging, pH modulation, freeze-thaw cycling, n-butanol dehydration, evaporation drying, and microwave heating, have enabled foundational advances but are constrained by slow kinetics, compromised structural uniformity and especially harsh reaction conditions, making them unsuitable for in situ tracking of biological events. This concept article introduces acoustic levitation synthesis as a groundbreaking alternative, uniquely addressing these limitations through a rapid, green, and highly controllable process. By leveraging non-contact acoustic radiation forces, this method enables the synthesis of ultrahigh-density SNAs within minutes under ambient conditions, eliminating the need for toxic reagents or energy-intensive steps. The resulting SNAs exhibit superior homogeneity and stability compared to conventional approaches. We critically evaluate the conceptual novelty and limitations of this technique. Potential applications in surface-enhanced Raman spectroscopy (SERS) and targeted therapeutics are highlighted, positioning acoustic levitation as a transformative tool for next-generation nanobiotechnology.

Effect of DNA Density on Nucleic Acid Detection Using Cross-Linking Aggregation of DNA-Modified Gold Nanoparticles

Gold nanoparticles (AuNPs) have been utilized as colorimetric biosensors by which target molecule-induced AuNP aggregation is recognized by a color change from red to blue. Particularly, single-stranded DNA (ssDNA)-immobilized AuNPs (ssDNA-AuNPs) have been applied to genetic diagnosis. Herein, we investigated the effect of the density of immobilized ssDNA on the sensitivity of the target ssDNA detection using two different cross-linking aggregation models of ssDNA-AuNPs, i.e., the unidirectional (UD) type and bidirectional (BD) type. We demonstrated that target ssDNA detection was more sensitive in both types of aggregation models when smaller amounts of immobilized ssDNA were used. Interestingly, the UD type was more sensitive in detecting the target than the BD type possibly due to the number of cross-links. It was also shown that the sensitivity differed depending upon the number of bases between the AuNPs at higher DNA density. Our results indicate that control of immobilized probe ssDNA density improves the detection sensitivity and duplex formation ratio in cross-linking aggregation.

Organic Modulators Enable Morphological Diversity in Colloidal Crystals Engineered with DNA

Colloidal crystal engineering with DNA is a powerful way of generating a wide variety of crystals spanning over 90 different symmetries. However, in many cases, crystals with well-defined habits are difficult, if not impossible, to make, in part due to rapid crystal defect formation and propagation. This is especially true in the case of face-centered cubic (FCC) structures. Herein, we report a strategy that uses formamide as a chemical modulator to slow down colloidal crystal growth, which decreases defect formation and yields higher-quality crystals. Formamide forms hydrogen bonds with DNA bases and destabilizes the DNA duplex; in the context of colloidal crystallization, formamide leads to the disassembly of undercoordinated particles (defect architectures) and facilitates their reassembly into structures with the maximum number of nearest-neighbor contacts and DNA bonds. When targeting an FCC lattice comprised of DNA-modified spherical 20 nm particles, formamide promotes the formation of its Wulff polyhedron (a truncated octahedron), never observed before in colloidal crystal engineering with DNA. Importantly, kinetic habits, including tetrahedra, octahedra, icosahedra, and decahedra, are also observed depending on formamide concentration.

Advanced Synthesis of Spherical Nucleic Acids: A Limit-Pursuing Game with Broad Implications

Spherical nucleic acids (SNAs) consist of DNA strands arranged radially and packed densely on the surface of nanoparticles. Due to their unique properties, which are not found in naturally occurring linear or circular DNA, SNAs have gained widespread attention in fields such as sensing, nanomedicine, and colloidal assembly. The rapidly evolving applications of SNAs have driven a modernization of their syntheses to meet different needs. Recently, several advanced approaches have emerged, enabling ultrafast, quantitative, and low-cost SNA synthesis with maximal DNA grafting through "counterintuitive" processes like freezing and dehydration. This concept paper discusses these critical developments from a synthetic perspective, focusing on their underlying mechanisms and broad implications, with a goal of inspiring future research in related fields.

Transforming Medicine: Cutting-Edge Applications of Nanoscale Materials in Drug Delivery

Since their inception in the early 1960s, the development and use of nanoscale materials have progressed tremendously, and their roles in diverse fields ranging from human health to energy and electronics are undeniable. The application of nanotechnology inventions has revolutionized many aspects of everyday life including various medical applications and specifically drug delivery systems, maximizing the therapeutic efficacy of the contained drugs by means of bioavailability enhancement or minimization of adverse effects. In this review, we utilize the CAS Content Collection, a vast repository of scientific information extracted from journal and patent publications, to analyze trends in nanoscience research relevant to drug delivery in an effort to provide a comprehensive and detailed picture of the use of nanotechnology in this field. We examine the publication landscape in the area to provide insights into current knowledge advances and developments. We review the major classes of nanosized drug delivery systems, their delivery routes, and targeted diseases. We outline the most discussed concepts and assess the advantages of various nanocarriers. The objective of this review is to provide a broad overview of the evolving landscape of current knowledge regarding nanosized drug delivery systems, to outline challenges, and to evaluate growth opportunities. The merit of the review stems from the extensive, wide-ranging coverage of the most up-to-date scientific information, allowing unmatched breadth of landscape analysis and in-depth insights.

Synthesis of metallic nanoparticles using biometabolites: mechanisms and applications

Bio-metabolites have played a crucial role in the recent green synthesis of nanoparticles, resulting in more versatile, safer, and effective nanoparticles. Various primary and secondary metabolites, such as proteins, carbohydrates, lipids, nucleic acids, enzymes, vitamins, organic acids, alkaloids, flavonoids, and terpenes, have demonstrated strong metal reduction and stabilization properties that can be utilized to synthesize nanomaterials and influence their characters. While physical and chemical methods were previously used to synthesize these nanomaterials, their drawbacks, including high energy consumption, elevated cost, lower yield, and the use of toxic chemicals, have led to a shift towards eco-friendly, rapid, and efficient alternatives. Biomolecules act as reducing agents through deprotonation, nucleophilic reactions, transesterification reactions, ligand binding, and chelation mechanisms, which help sequester metal ions into stable metal nanoparticles (NPs). Engineered NPs have potential applications in various fields due to their optical, electronic, and magnetic properties, offering improved performance compared to bulkier counterparts. NPs can be used in medicine, food and agriculture, chemical catalysts, energy harvesting, electronics, etc. This review provides an overview of the role of primary and secondary metabolites in creating effective nanostructures and their potential applications.

Thermal Transport through CTAB- and MTAB-Functionalized Gold Interfaces Using Molecular Dynamics Simulations

Thermal transport coefficients, notably the interfacial thermal conductance, were determined in planar and spherical gold interfaces functionalized with CTAB (cetyltrimethylammonium bromide) or MTAB (16-mercapto-hexadecyl-trimethylammonium bromide) using reverse nonequilibrium molecular dynamics (RNEMD) methods. The systems of interest included (111), (110), and (100) planar facets as well as nanospheres (r = 10 Å). The effect of metal polarizability was investigated through the implementation of the density-readjusted embedded atom model (DR-EAM), a polarizable metal potential. We find that conductance is higher in MTAB-capped interfaces, due in large part to the metal-to-ligand coupling provided by the Au-S bond. Alternatively, CTAB does not couple strongly with either the metal or the solvent, and it is largely a barrier to heat transfer, resulting in a much lower interfacial thermal conductance. Through analysis of physical contact between the ligand and the solvent, we find that there is significantly more overlap in the MTAB systems than the CTAB systems, mirroring the trends we observed in the conductance.

Shape-Dependent Locomotion of DNA-Linked Magnetic Nanoparticle Films

The shape-dependent aero- and hydro-dynamics found in nature have been adopted in a wide range of areas spanning from daily transportation to forefront biomedical research. Here, we report DNA-linked nanoparticle films exhibiting shape-dependent magnetic locomotion, controlled by DNA sequences. Fabricated through a DNA-directed layer-by-layer assembly of iron oxide and gold nanoparticles, the multifunctional films exhibit rotational and translational motions under magnetic fields, along with reversible shape morphing via DNA strand exchange reactions. Notably, the shape of the film significantly influences its magnetic responsiveness, attributable to shape-dependent drag forces acting on mesoscopic films. The distinctive shape dependence combined with the shape-changing capability offers an approach to regulate magnetic locomotion within a constant magnetic field, as demonstrated here through the go and stop motion of nanoparticle films without altering the magnetic field.

Formulation Optimization and Characterization of Tizanidine Hydrochloride-loaded Gold Nanoparticles Using Quality by Design Approach

BACKGROUND

Gold nanoparticles (GNP) have been used extensively in cancer biologics and as drug carrier systems for improved pharmacokinetics and effective therapeutic action. GNPs also ensure reliable diagnosis with sensitive imaging.

OBJECTIVES

This study aimed to synthesize tizanidine hydrochloride (TZN)-biodegradable gold (Au) nanoparticles by the reduction of chloroauric acid (HAuCl4) with trisodium citrate using a microwave synthesizer and quality by design approach.

METHODS

The formulation method used was optimized using a 32 (two-factor, three-level design) factorial experiment. Temperature (X1) and concentration of gold salt (X2) were the two independent factors, and particle size (Y1), Percent drug entrapment efficiency (Y2), and polydispersity index (Y3) were the responses recorded for the study.

RESULTS

The results of the study revealed that the optimized nanoparticles (TGN8) had a particle size (Y1) of 195 ± 1.2 nm, a polydispersity index of 0.2, and entrapment efficiency of 99.0 ± 2.9% at an optimized concentration of 14 mM gold salt (X1) and 100°C temperature (X2). Atomic Force Microscopy showed the spherical shape particles. In vitro drug release was found to be 62.1 ± 0.5% release of TZN in simulated gastric buffer (pH 1.2) and 45.5 ± 2.8% in physiological buffer (pH 7.4).

CONCLUSION

Overall, the study identified the optimal formulation conditions for TZN GNPs by considering the effects of independent variables on desired responses.

Swarm Autonomy: From Agent Functionalization to Machine Intelligence

Swarm behaviors are common in nature, where individual organisms collaborate via perception, communication, and adaptation. Emulating these dynamics, large groups of active agents can self-organize through localized interactions, giving rise to complex swarm behaviors, which exhibit potential for applications across various domains. This review presents a comprehensive summary and perspective of synthetic swarms, to bridge the gap between the microscale individual agents and potential applications of synthetic swarms. It is begun by examining active agents, the fundamental units of synthetic swarms, to understand the origins of their motility and functionality in the presence of external stimuli. Then inter-agent communications and agent-environment communications that contribute to the swarm generation are summarized. Furthermore, the swarm behaviors reported to date and the emergence of machine intelligence within these behaviors are reviewed. Eventually, the applications enabled by distinct synthetic swarms are summarized. By discussing the emergent machine intelligence in swarm behaviors, insights are offered into the design and deployment of autonomous synthetic swarms for real-world applications.

Excellent properties of NaF and NaBr induced DNA/gold nanoparticle conjugation system: Better stability, shorter modified time, and higher loading capacity

The functionalization of gold nanoparticle (AuNP) is the key procedure for the biochemical and biomedical application. The conventional salt-aging method requires the stepwise additions of NaCl and excessive thiolated DNA, mainly due to the poor tolerance of the DNA/AuNP mixture toward NaCl. Herein, we found that NaF is capable of improving the stability for the modification of AuNP with different bases of DNA sequences (poly A/T/C/G), and allows for adding up with a high concentration of 200 mM at one time, which greatly reduces the total modification time to 0.5-1 h. Intriguingly, the introduction of NaBr effectively increases the DNA loading capacity. Besides the advantages of NaF and NaBr, the modification performance is improved via the introduction of the oligo A/T spacer for the G-rich DNA sequences. Furthermore, this method shows the superiority to another two methods (pH 3-based and salt-aging) in terms of the loading capacity or sequence components.

In Vivo Interactions of Nucleic Acid Nanostructures With Cells

Nucleic acid nanostructures, derived from the assembly of nucleic acid building blocks (e.g., plasmids and oligonucleotides), are important intracellular carriers of therapeutic cargoes widely utilized in preclinical nanomedicine applications, yet their clinical translation remains scarce. In the era of "translational nucleic acid nanotechnology", a deeper mechanistic understanding of the interactions of nucleic acid nanostructures with cells in vivo will guide the development of more efficacious nanomedicines. This review showcases the recent progress in dissecting the in vivo interactions of four key types of nucleic acid nanostructures (i.e., tile-based, origami, spherical nucleic acid, and nucleic acid nanogel) with cells in rodents over the past five years. Emphasis lies on the cellular-level distribution of nucleic acid nanostructures in various organs and tissues and the cellular responses induced by their cellular entry. Next, in the spirit of preclinical translation, this review features the latest interactions of nucleic acid nanostructures with cells in large animals and humans. Finally, the review offers directions for studying the interactions of nucleic acid nanostructures with cells from both materials and biology perspectives and concludes with some regulatory updates.

Dependencies between effective parameters in coarse-grained models for phase separation of DNA-based fluids

DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, very little is known about the emergence of structure on larger scales in DNA fluids. The fact that polymeric DNA fluids can undergo phase separation into dense fluid and dilute gas opens avenues to design hierachical and multifarious assemblies. Here, we investigate to which extent the phase behavior of single-stranded DNA fluids can be captured by a minimal model of semiflexible charged homopolymers while neglecting specific hybridization interactions. We first characterize the single-polymer behavior and then perform direct coexistence simulations to test the model against experimental data. While low-resolution models show great promise to bridge the gap to relevant length and time scales, obtaining consistent and transferable parameters is challenging. In particular, we conclude that counterions not only determine the effective range of direct electrostatic interactions but also contribute to the effective attractions.

DNA-amphiphilic nanostructures: synthesis, characterization and applications

DNA's extraordinary potential reaches far beyond its role as a carrier of genetic information. It serves as a remarkably adaptable structural foundation for constructing intricate nanostructures with a diverse range of functionalities. This inherent programmability sets DNA apart from other biomolecules like peptides, proteins, and small molecules. By covalently attaching DNA to synthetic hydrophobic moieties, researchers create DNA amphiphiles capable of interacting with artificial lipid bilayers and cell membranes. These hybrid structures have rapidly gained prominence due to their promising potential in the medical field. This review provides a comprehensive overview of the latest advancements in the synthesis of DNA amphiphiles and their assembly into well-defined nanostructures. It explores the diverse applications of these nanostructures across various medical domains, including targeted drug delivery, innovative immunotherapies, and gene-silencing techniques. Moreover, the review delves into the current challenges and prospects of this rapidly evolving field, highlighting the potential of DNA hybrid materials to revolutionize medical treatments and diagnostics. By addressing the limitations and exploring new avenues of research, scientists aim to unlock the full potential of DNA nanotechnology for the benefit of human health.

DNA-Regulated Multi-Protein Complement Control

In nature, the interactions between proteins and their complements/substrates can dictate complex functions. Herein, we explore how DNA on nucleic acid modified proteins can be used as scaffolds to deliberately control interactions with a peptide complement (by adjusting length, sequence, and rigidity). As model systems, split GFPs were covalently connected through DNA scaffolds (36-58 bp). Increasing the length or decreasing the rigidity of the DNA scaffold (through removal of the duplex) increases the extent of intramolecular protein binding (up to 7.5-fold) between these GFP fragments. Independent and dynamic control over functional outputs can also be regulated by DNA hybridization; a multi-protein (split CFP and YFP) architecture was synthesized and characterized by fluorescence. This ternary construct shows that DNA displacement strands in different stoichiometric ratios can be used deliberately to regulate competitive binding between two unique sets of proteins. These studies establish a foundation for creating new classes of biological machinery based upon the concept of DNA-regulated multi-protein complement control.

Freezing Functional Nucleic Acids: From Molecular Reactions to Surface Immobilization

Biochemical reactions are typically slowed down by decreasing temperature. However, accelerated reaction kinetics have been observed for a long time. More recent examples have highlighted the unique role of freezing in fabricating supermaterials, degrading environmental contaminants, and accelerating bioreactions. Functional nucleic acids are DNA or RNA oligonucleotides with versatile properties, including target recognition, catalysis, and molecular co4mputing. In this review, we discuss the current observations and understanding of freezing-facilitated reactions involving functional nucleic acids. Molecular reactions such as ligation/conjugation, cleavage, and hybridization are discussed. Moreover, freezing-induced DNA-nanoparticle conjugations are introduced. Then, we describe our effect in immobilizing DNA on bulk surfaces. Finally, we address some critical questions and research opportunities in the field.

Rapid Thermal Drying Synthesis of Nonthiolated Spherical Nucleic Acids with Stability Rivaling Thiolated DNA

Attaching DNA oligonucleotides to gold nanoparticles (AuNPs) to prepare spherical nucleic acids (SNAs) has offered tremendous insights into surface chemistry with resulting bioconjugates serving as critical reagents in biosensors and nanotechnology. While thiolated DNA is generally required to achieve stable conjugates, we herein communicate that using a thermal drying method, a high DNA density and excellent SNA stability was achieved using nonthiolated DNA, rivaling the performance of thiolated DNA such as surviving 1 M NaCl, 2 month stability in 0.3 M NaCl and working in 50 % serum. A poly-adenine block with as few as two consecutive terminal adenine bases is sufficient for anchoring on AuNPs. By side-by-side comparison with the salt-aging method, the conjugation mechanism was attributed to competitive adenine adsorption at high temperature along with an extremely high DNA concentration upon drying. Bioanalytical applications of nonthiolated SNAs were validated in both solution and paper-based sensor platforms, facilitating cost-effective applications for SNAs.

Understanding orientational disorder in crystalline assemblies of hard convex polyhedra

Spontaneous self-assembly of hard convex polyhedra is known to form orientationally disordered crystalline phases, where particle orientations do not follow the same pattern as the positional arrangement of the crystal. A distinct type of orientational phase with discrete rotational mobility has been reported in hard particle systems. In this paper, we present a new analysis method for characterizing the orientational phase of a crystal, which is based on algorithmic detection of unique orientations. Using this method, we collected complete statistics of discrete orientations along the Monte Carlo simulation trajectories and observed that particles were equally partitioned among them, with specific values of pairwise orientational differences. These features remained constant across the pressure range and did not depend on rotational mobility. The discrete mobility was characteristic of a distinct equilibrium thermodynamic phase, qualitatively different from the freely rotating plastic phase with continuous orientations. The high pressure behavior with frozen particle orientations was part of that same description and not a non-equilibrium arrested state. We introduced a precise notion of orientational order and demonstrated that the system was maximally disordered at the level of a unit cell, even though individual particles could only take a few discrete orientations. We report the existence of this phase in five polyhedral shapes and in systematically curated shape families constructed around two of them. The symmetry mismatch between the particle and the crystallographic point groups was found to be a predictive indicator for the occurrence of this phase.

Microcrystal Growth Pathways Investigated with Machine Learning Segmentation and Classification in Scanning Electron Microscopy

Advances in electron microscopy have revolutionized material characterization on the nano- and microscales, providing important insights into local ordering, structure, and size and quality distributions. While shape and size can be rigorously quantified through microscopy, it is often limited to local structure analysis and fails to describe bulk sample quality. Herein, a flexible machine learning (ML) tool is described that can segment and classify faceted crystals in scanning electron microscopy (SEM) micrographs to determine sample quality through the crystal size and product distribution. As a case study, this tool was applied to investigate crystal growth pathways (classical nucleation and growth compared to nonclassical growth) in DNA-mediated nanoparticle assembly through size and product (single crystal, fused crystal, or noncrystal) distribution of samples containing over 13000 colloidal crystal products. Strong DNA bond strengths (controlled by DNA sequence) lead to fast nucleation that exhausts the monomer concentration, resulting in smaller colloidal crystals. Alternatively, increased thermal energy and crystallization time lead to nonclassical crystallization pathways (coalescence) that result in larger colloidal crystals. This tool is useful since experimental conditions can now be deliberately identified to control colloidal crystal size and size distribution, important considerations for researchers interested in designing and synthesizing colloidal crystal metamaterials.

Plasmonic nanoparticle sensors: current progress, challenges, and future prospects

Plasmonic nanoparticles (NPs) have played a significant role in the evolution of modern nanoscience and nanotechnology in terms of colloidal synthesis, general understanding of nanocrystal growth mechanisms, and their impact in a wide range of applications. They exhibit strong visible colors due to localized surface plasmon resonance (LSPR) that depends on their size, shape, composition, and the surrounding dielectric environment. Under resonant excitation, the LSPR of plasmonic NPs leads to a strong field enhancement near their surfaces and thus enhances various light-matter interactions. These unique optical properties of plasmonic NPs have been used to design chemical and biological sensors. Over the last few decades, colloidal plasmonic NPs have been greatly exploited in sensing applications through LSPR shifts (colorimetry), surface-enhanced Raman scattering, surface-enhanced fluorescence, and chiroptical activity. Although colloidal plasmonic NPs have emerged at the forefront of nanobiosensors, there are still several important challenges to be addressed for the realization of plasmonic NP-based sensor kits for routine use in daily life. In this comprehensive review, researchers of different disciplines (colloidal and analytical chemistry, biology, physics, and medicine) have joined together to summarize the past, present, and future of plasmonic NP-based sensors in terms of different sensing platforms, understanding of the sensing mechanisms, different chemical and biological analytes, and the expected future technologies. This review is expected to guide the researchers currently working in this field and inspire future generations of scientists to join this compelling research field and its branches.

Gold Nanoprobes for Robust Colorimetric Detection of Nucleic Acid Sequences Related to Disease Diagnostics

Gold nanoparticles (AuNPs) are highly attractive for applications in the field of biosensing, particularly for colorimetric nucleic acid detection. Their unique optical properties, which are highly sensitive to changes in their environment, make them ideal candidates for developing simple, rapid, and cost-effective assays. When functionalized with oligonucleotides (Au-nanoprobes), they can undergo aggregation or dispersion in the presence of complementary sequences, leading to distinct color changes that serve as a visual signal for detection. Aggregation-based assays offer significant advantages over other homogeneous assays, such as fluorescence-based methods, namely, label-free protocols, rapid interactions in homogeneous solutions, and detection by the naked eye or using low-cost instruments. Despite promising results, the application of Au-nanoprobe-based colorimetric assays in complex biological matrices faces several challenges. The most significant are related to the colloidal stability and oligonucleotide functionalization of the Au-nanoprobes but also to the mode of detection. The type of functionalization method, type of spacer, the oligo-AuNPs ratio, changes in pH, temperature, or ionic strength influence the Au-nanoprobe colloidal stability and thus the performance of the assay. This review elucidates characteristics of the Au-nanoprobes that are determined for colorimetric gold nanoparticles (AuNPs)-based nucleic acid detection, and how they influence the sensitivity and specificity of the colorimetric assay. These characteristics of the assay are fundamental to developing low-cost, robust biomedical sensors that perform effectively in biological fluids.

Structural Evolution Study of Titanium-Vanadium-Niobium Nanoparticles from Single to Multicomponent Systems

In this article, the revised basin-hopping with mirror-rotation sampling combined with density functional theory, which was proposed by our previous study, was used to study the structural property of Ti n (n = 3m, m = 1-7), V n (n = 3m, m = 1-7), Nb n (n = 3m, m = 1-7), and Ti n V n Nb n (n = 1-7) systems. We found that equiatomic Ti n V n Nb n (n = 1-7) systems do not change their lowest energy structures relative to the same size Ti n (n = 3m, m = 1-7), V n (n = 3m, m = 1-7), and Nb n (n = 3m, m = 1-7) systems, and this indicates that the nanoparticles composed of titanium, vanadium, or niobium elements may have similar energy morphologies when the atomic number is the same. Based on the low-energy structural similarity of titanium-vanadium-niobium systems between single and multicomponent, we used the element space position replacement (ESPR) method to reconstruct the low-energy structure of Ti n V n Nb n (n = 1-7) systems. For the Ti7V7Nb7 system, the average sampling step of 10 separate searches of the BH-MRS method is 1226 more than that of the ESPR method to find the lowest energy structure (six-ring layered structure). The electronic property calculation shows that using equiatomic vanadium and niobium elements to replace titanium element in the Ti n (n = 3m, m = 1-7) system may not change its stability, and the Ti n (n = 3m, m = 1-7) system has better electron trapping ability than V n (n = 3m, m = 1-7), Nb n (n = 3m, m = 1-7), and Ti n V n Nb n (n = 1-7) systems. Our method and results can be helpful for the design of nanostructures of transition metals with better catalytic properties.

Implementation of Digital Computing by Colloidal Crystal Engineering with DNA

Toehold-mediated strand displacement (TMSD) provides a versatile toolbox for developing DNA digital computing systems. Although different logic circuits with diverse functions have achieved good performance in terms of complexity and scalability, most previous DNA logic circuits perform information processing only at the molecular level, and nonspecific signal leakages are often difficult to avoid. Here, we demonstrate the feasibility of constructing leakless digital computing systems in three-dimensionally ordered colloidal supercrystals. These systems possess a unique signal leakage resistance by integrating different TMSD-based logic gates with the catalytic assembly of DNA-functionalized gold colloids. A complete set of basic Boolean logic gates and different cascaded logic circuits is constructed on the basis of the catalytic assembly strategy enabled by a facilely designed catassembler, where the output signals are recognized by determining whether specific colloidal supercrystals are formed or not. In addition, a half adder is built through a combination of XOR and AND logic gates with two distinct crystal types as readouts. Finally, a leakless two-digit DNA keypad lock for information security protection is demonstrated. The combination of TMSD-based logic circuits with the universal nanoparticle catalytic assembly offers the possibility to develop highly complicated and leakage-free digital computing systems and promotes macroscopic colloidal superlattice materials with programmable logic functions.

Towards the Development of an Optical Biosensor for the Detection of Human Blood for Forensic Analysis

Blood is a common biological fluid in forensic investigations, offering significant evidential value. Currently employed presumptive blood tests often lack specificity and are sample destructive, which can compromise downstream analysis. Within this study, the development of an optical biosensor for detecting human red blood cells (RBCs) has been explored to address such limitations. Aptamer-based biosensors, termed aptasensors, offer a promising alternative due to their high specificity and affinity for target analytes. Aptamers are short, single-stranded DNA or RNA sequences that form stable three-dimensional structures, allowing them to bind to specific targets selectively. A nanoflare design has been employed within this work, consisting of a quenching gold nanoparticle (AuNP), DNA aptamer sequences, and complementary fluorophore-labelled flares operating through a fluorescence resonance energy transfer (FRET) mechanism. In the presence of RBCs, the aptamer-flare complex is disrupted, restoring fluorescence and indicating the presence of blood. Two aptamers, N1 and BB1, with a demonstrated binding affinity to RBCs, were selected for inclusion within the nanoflare. This study aimed to optimise three features of the design: aptamer conjugation to AuNPs, aptamer hybridisation to complementary flares, and flare displacement in the presence of RBCs. Fluorescence restoration was achieved with both the N1 and BB1 nanoflares, demonstrating the potential for a functional biosensor to be utilised within the forensic workflow. It is hoped that introducing such an aptasensor could enhance the forensic workflow. This aptasensor could replace current tests with a specific and sensitive reagent that can be used for real-time detection, improving the standard of forensic blood analysis.

Surface Functionalization of Gold Nanoparticles Using Alkyne Derivatives: Applications in Chemical Sensing

Colloidal gold nanoparticles (AuNPs) are important nanomaterials for chemical sensing and therapeutics. For their application, it is vital to develop a reliable and robust surface functionalization method that can be applied to diverse functional molecules and offer better stability under harsh biological conditions. Currently, thiol (SH) is the most commonly used functional group for forming stable covalent bonds with AuNPs. However, thiolated molecules typically require complicated preparation procedures, are susceptible to oxidation, and are not compatible with many electrophiles and reducing groups. In this study, we report that surface functionalization of AuNPs can be achieved using alkyne derivatives, which exhibit several advantages over classical thiolation and peptide-bond methods, including straightforward preparation of alkyne derivatives, rapid and simple conjugation in buffers and complex media, higher conjugation efficiency, long-term stability, and resistance to decomposition under harsh conditions. Several alkynylated biotin and fluorescein derivatives are prepared, and the alkynylated-AuNPs are characterized using a lateral flow assay, gel electrophoresis, and spectroscopy techniques to investigate the conjugation efficiencies, size distributions, protein interaction properties, and binding mode of the Au-alkyne bond. We also demonstrate that alkynylated-AuNPs can be used for the sensitive detection of hydrogen peroxide and streptavidin proteins.

High Temperature, Isothermal Growth Promotes Close Packing and Thermal Stability in DNA-Engineered Colloidal Crystals

We report a strategy to accelerate the synthesis and increase the crystallinity of colloidal crystals (CCs) engineered with DNA. Specifically, by holding the DNA-modified Au particle building blocks above the Tm of the DNA bonding elements (i.e., free from the particles), but slightly below the Tm of the anticipated CC during the assembly process, crystallinity is increased, and enthalpically favored phases with high degrees of facet registration are observed. We studied the utility of this approach with systems for which the commonly adopted slow-cooling approach yielded primarily amorphous aggregates. In particular, we used it to synthesize high-volume fraction CCs from large (80 nm) anisotropic nanoparticles (cubes and rhombic dodecahedra) with short (<14 nm) DNA designed to restrict the degrees of freedom for the DNA bonds and maintain the anisotropy of the particle building block. Small-angle X-ray scattering and electron microscopy studies show that the crystalline phases synthesized via this method are more thermally stable than their corresponding aggregate phases, likely due to an increased number of DNA-DNA bonds between particles. Crystal size tunability (between 0.5 and 15 μm edge lengths) and epitaxial growth were demonstrated using this strategy by modulating the NaCl concentration in tandem with previously synthesized CC nuclei. Taken together, this isothermal strategy demonstrates how to deliberately crystallize a wide variety of anisotropic colloidal materials and expands the phase space accessible to nanoparticles modified with DNA.

Click-Chemistry-Enabled Functionalization of Cellulose Nanocrystals with Single-Stranded DNA for Directed Assembly

Controlling the self-assembly of cellulose nanocrystals (CNCs) requires precise control over their surface chemistry for the directed assembly of advanced nanocomposites with tailored mechanical, thermal, and optical properties. In this work, in contrast to traditional chemistries, we conducted highly selective click-chemistry functionalization of cellulose nanocrystals with complementary DNA strands via a three-step hybridization-guided process. By grafting terminally functionalized oligonucleotides through copper-free click chemistry, we successfully facilitated the assembly of brushlike DNA-modified CNCs into bundled nanostructures with distinct chiral optical dichroism in thin films. The complexation behavior of grafted DNA chains during the evaporation-driven formation of ultrathin films demonstrates the potential for mediating chiral interactions between the DNA-branched nanocrystals and their assembly into chiral bundles. Furthermore, we discuss the future directions and challenges that include new avenues for the development of functional, responsive, and bioderived nanostructures capable of dynamic reconfiguration via selective complexation, further surface modification strategies, mitigating diverse CNC aggregation, and exploring environmental conditions for the CNC-DNA assembly.

Highly sensitive and specific electrochemical biosensor for direct detection of hepatitis C virus RNA in clinical samples using DNA strand displacement

Hepatitis C virus (HCV) is a common blood-borne infection that can lead to long-term illnesses such as hepatocellular cancer and liver cirrhosis. Early diagnosis is crucial for effective management, as no vaccine is available for preventing HCV infection. However, the high cost and complexity of current molecular diagnostic tools hinder efforts to achieve early diagnosis and prevent transmission, particularly in resource-limited settings. We developed a novel electrochemical biosensor for point-of-care testing (POCT) of HCV RNA. The sensor utilizes a strand displacement method, where the target RNA displaces a gold nanoparticle-labeled reporter probe (AuRP) from a pre-hybridized duplex with a magnetic nanoparticle (MNP)-labeled capture probe. The amount of displaced AuRP, detected using differential pulse anodic stripping voltammetry (DPASV), is directly proportional to the target RNA concentration. The biosensor exhibited excellent analytical performance, with a detection limit of 4 fM for synthetic targets and 43 ng/µL for RT-PCR products. Importantly, it successfully detected HCV RNA directly in clinical plasma samples without the need for RNA extraction or amplification. The sensor was used to analyze 30 RNA samples from HCV-positive patients, 20 cDNA samples from viral RNA, 30 HCV-positive plasma samples, and 22 HCV-negative plasma samples. The sensor results show good concordance with the RT-PCR results, demonstrating the sensor's potential for detecting HCV in clinical samples.

Hopping and crawling DNA-coated colloids

Understanding the motion of particles with multivalent ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or roll, depending on the study. We shed light on this problem by observing DNA-coated colloids diffusing near surfaces coated with complementary strands for a wide array of coating designs. We find colloids rapidly switch between 2 modes: They hop-with long and fast steps-and crawl-with short and slow steps. Both modes occur at all temperatures around the melting point and over various designs. The particles become increasingly subdiffusive as temperature decreases, in line with subsequent velocity steps becoming increasingly anticorrelated, corresponding to switchbacks in the trajectories. Overall, crawling (or hopping) phases are more predominant at low (or high) temperatures; crawling is also more efficient at low temperatures than hopping to cover large distances. We rationalize this behavior within a simple model: At lower temperatures, the number of bound strands increases, and detachment of all bonds is unlikely, hence, hopping is prevented and crawling favored. We thus reveal the mechanism behind a common design rule relying on increased strand density for long-range self-assembly: Dense strands on surfaces are required to enable crawling, possibly facilitating particle rearrangements.

Visualizing Macrophage Polarization through Fluorescent mRNA Profiling

Macrophages, known for their phenotypic plasticity, play a critical role in maintaining homeostasis and inflammation-related pathogenesis. Although identifying diverse macrophage phenotypes holds promise for enhancing diagnoses and treatments of diseases mediated by macrophages, existing methodologies for differentiating macrophages often lack precision. They are limited by the cumbersome procedures that require large-scale equipment, such as flow cytometry and transcriptomic analysis. In this context, we have engineered fluorescent polyadenine (polyA)-mediated sticky flares that enable practical visualization of macrophages. This technology facilitates the highly sensitive detection of macrophage phenotypes through the specific recognition of intracellular mRNAs, permitting in situ imaging. Our approach demonstrates the potential for determining macrophage polarization status at the single-cell level within dynamic immune microenvironments, thereby providing crucial diagnostic and prognostic information that could guide the development of tailored treatments for macrophage-related diseases in personalized medicine.