Accessible hotspots for single-protein SERS in DNA-origami assembled gold nanorod dimers with tip-to-tip alignment

Nucleic acid-mediated SERS Biosensors: Signal enhancement strategies and applications

Surface Enhanced Raman Spectroscopy (SERS) is a powerful spectroscopic analysis technique applied in various fields due to its high selectivity, ultra-high sensitivity, and non-destructiveness. As natural biological macromolecules, nucleic acids perform a significant role in SERS biosensing. In this review, we first summarize how nucleic acids mediate the signal enhancement of SERS biosensors from three aspects: substrate self-assembly, analyte biorecognition, and molecular amplification. Among them, SERS substrates can be self-assembled by both DNA modification and coordination or electrostatic interactions. In the field of biorecognition, analyte biorecognition based on three nucleic acid recognition elements can enhance SERS signals by regulating the distance of analytes or Raman reporter molecules to the SERS substrate. In addition, nucleic acid-based enzyme and enzyme-free amplification can enhance SERS signals by enlarging the quantity of analytes or its nucleic acid intermediates. Subsequently, multidimensional applications of nucleic acid-mediated SERS signal enhancement in biomedicine, food safety, and environmental monitoring are listed. Finally, the current challenges and future exploration of nucleic acid-mediated SERS signal enhancement are discussed.

Large-Scale Fabrication of 5 nm Plasmonic Hybrid Nanoslit Arrays

Surface plasmon resonance harnessed through nanometer-scale metallic gaps generates intense near-fields, unlocking vast potential for applications in nanophotonics and biosensing. However, the scarcity of scalable and reproducible nanofabrication techniques capable of achieving a sub-10 nm gap remains a significant barrier to widespread implementation. Here, we present a high-throughput method combining deep-UV interference lithography, molecular self-assembly, and peeling to fabricate large-scale arrays of an ∼ 5 nm Au-Ag hybrid nanoslit. These arrays serve as highly effective substrates for surface-enhanced Raman spectroscopy (SERS), demonstrating the ability to detect rhodamine 6G at concentrations as low as 1 pM with an analytical enhancement factor of 2.2 × 107. Specifically, the hybrid nanoslit arrays exhibit significantly higher (by 2.6-fold) field enhancements than monolithic nanoslit arrays due to the in-phase hybridization mode in Au-Ag nanoslit. Our cost-effective, large-scale approach overcomes traditional scalability and hybrid patterning barriers, offering transformative potential for sensitive, reliable SERS-based detection platforms.

Research progress on regulation strategies for surface-enhanced Raman spectroscopy

As a highly sensitive analytical technology, surface enhanced Raman spectroscopy (SERS) based on localized surface plasmon resonance has been widely explored in the field of environment monitoring, food safety, material identification and biomedicine. In the field of biosensing, the design of sensing models, the regulation of enhancement factors (EFs), and the stability of detection results have always been crucial research keys. Progress in these areas has continuously expanded the application scope of SERS technology and improved the feasibility of its application. Among them, the regulation of EFs through physical enhancement and chemical enhancement is a crucial point in improving the performance of SERS. Starting from the physicochemical mechanism, this review discusses the relevant influencing parameters and then summarizes the latest regulation strategies based on the above theory, as well as special regulation methods such as E-SERS. A diverse array of regulation strategies underpinned by the SERS enhancement mechanism have been effectively harnessed to amplify the EF of the SERS system. These include a wide spectrum of metal nanostructures based on the electromagnetic mechanism (EM), as well as regulation approaches predicated on the chemical mechanism (CM), such as energy-level manipulation, defect engineering, and material coupling. In addition, it encompasses specialized regulation methods such as analyte pre-concentration. This article focuses on summarizing the principal regulation approaches that have significantly impacted SERS enhancement in recent years, complemented by specialized regulation methods, with the hope of facilitating smoother progress in future work related to SERS.

DNA-mediated precise regulation of SERS hotspots for biosensing and bioimaging

Surface-enhanced Raman scattering (SERS) is a powerful analytical technique, where the creation of "hotspots" holds the key to unlocking sensitive, reproducible and reliable performance. DNA nanostructures, known for their unique predictability and exceptional programmability, have emerged as promising tools for the controllable assembly and precise regulation of SERS hotspots. In recent years, the application of DNA nanotechnology in the regulation of SERS hotspots has emerged as a research focus, but a comprehensive summary of this field is still lacking. This review begins by elucidating the mechanisms of localized surface plasmon resonance (LSPR) coupling and SERS enhancement, providing a theoretical foundation for the design principles and assembly strategies for SERS hotspots. Following this, general approaches for assembling static SERS hotspots using DNA structures of different dimensions as linkers or templates are explored. Subsequently, we delve into dynamic regulation strategies for SERS hotspots mediated by DNA structures, focusing on structural reconfiguration driven by DNA hybridization, toehold-mediated strand displacement (TMSD), and enzyme-catalyzed DNA allostery, and then summarize recent examples of DNA-mediated hotspot regulation in biosensing and bioimaging applications. Finally, we discuss future perspectives associated with the DNA-mediated precise regulation of SERS hotspots, underscoring the imperative for enhanced scalability, uniformity, and integration to pave the way for real-world applications.

Targeted molecular rapid SERS diagnosis in clinical human serum through aptamer origami-collapsed nanofingers chip

Surface-Enhanced Raman Scattering (SERS) offers great potential for label-free molecular diagnosis, especially in detecting disease biomarkers. However, the complexity of the biological environment in clinical human serum often significantly impairs detection accuracy. In this study, we present a highly effective SERS strategy utilizing aptamer origami-collapsed nanofingers for the precise qualitative and quantitative detection of specific targeted biomarkers in clinical serum. Here, the biomarker-specific aptamers are anchored to gold nanofingers, which then collapse during liquid evaporation, forming sub-nanometric gaps that enhance near-field strength. The serum is introduced directly into these stabilized nanofingers, where targeted biomarkers are selectively captured in aptamer hotspots, yielding pure Raman spectra of the biomarkers without interference from other serum molecules. The ratio of the biomarker's characteristic Raman peak to that of the aptamer allows for accurate quantification. This approach was validated with alpha-fetoprotein (AFP) for hepatocellular carcinoma and cardiac troponin I (cTnI) for acute myocardial infarction in clinical serum, achieving detection within 3 min. This strategy represents a significant advancement in SERS-based medical diagnostics, offering exceptional sensitivity and specificity in complex biological samples.

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.

Gold Tetrahedral Nanoframes with Mono-Rim or Dual-Rim Morphologies for Enhanced Near-Field Focusing in SERS

This study presents a synthesis method for Au tetrahedral nanoframes (Td NFs) through a rationally designed multiple-step process, followed by an investigation of their distinctively ordered self-assembly for enhanced performance in surface-enhanced Raman spectroscopy (SERS). Two distinct Au Td NF building blocks are synthesized, exhibiting mono-rim or dual-rim morphologies. The mono-rim structure lacks intra-nanogaps, whereas the dual-rim configuration features well-defined intra-nanogaps. The non-centrosymmetric Td NFs self-assemble into a distinctive antiparallel arrangement that alternates between the tip-up and face-up orientations of the Au Td NFs. This configuration results in the formation of both triply tip-to-tip and face-to-face nanogaps. The unique zigzag pattern exhibited strong electromagnetic field enhancement and extensive spatial hot zones, significantly amplifying near-field focusing and, consequently, the SERS effect. The near-field enhancement of Au Td NF assemblies is confirmed through finite element method simulations and experimentally validated by comparing bulk SERS measurements with those of Au octahedron NF assemblies, which tend to adopt a parallel face-to-tip alignment during assembly. Owing to the complex arrangement of multiple intra-nanogaps between the internal rim-to-rim interfaces and the four exposed facets, dual-rim Td NFs exhibited single-particle SERS activity, a capability not observed in analogous Td NFs with single rims.

Advances in Functional Nucleic Acid SERS Sensing Strategies

Functional nucleic acids constitute a distinct category of nucleic acids that diverge from conventional nucleic acid amplification methodologies. They are capable of forming intricate hybrid structures through Hoogsteen and reverse Hoogsteen hydrogen bonding interactions between double-stranded and single-stranded DNA, thereby broadening the spectrum of DNA interactions. In recent years, functional DNA/RNA-based surface-enhanced Raman spectroscopy (SERS) has emerged as a potent platform capable of ultrasensitive and multiplexed detection of a variety of analytes of interest. This review aims to elucidate the operational principles of several functional nucleic acids in SERS detection, including DNAzymes, G-quadruplexes, aptamers, CRISPR, origami etc., alongside the design methodologies and practical applications of functional DNA/RNA-based SERS sensing. Initially, an overview is summarized encompassing the structural attributes and SERS sensing mechanisms inherent to diverse functional DNA/RNA. Following this, various innovative strategies for constructing functional nucleic acid-based SERS sensors are illustrated in detail, aimed at improving the present detection capabilities. A comprehensive summing up is then conducted on the applications of these sensors in crucial fields, such as disease diagnosis, environmental monitoring, and food safety detection, with a particular focus on SERS sensitivity, specificity, and analytical versatility. Finally, conclusive remarks are offered along with an exploration of the existing challenges and prospective avenues for future research in this developed field.

Single-Molecule Detection via Pore Nanoconfinement of Covalent Organic Frameworks for Surface-Enhanced Raman Scattering

Surface-enhanced Raman scattering (SERS) offers significant advantages for single-molecule detection. However, stochastic molecular motion makes it challenging to consistently capture signals from single-molecule binding events, particularly in complex environments. Herein, we propose a novel SERS system via the pore nanoconfinement effect of covalent organic frameworks (COFs) to achieve reliable single-molecule detection. The self-assembled COF thin films on SERS metal substrates (Au/Ag) create a nanogap of 3 nm, allowing electric field enhancement. By precise tuning of the COF shell thickness, a molecular-scale pore volume is formed, effectively trapping individual molecules from molecular aggregates. Furthermore, the strong intermolecular forces within the COF pores significantly enhance the residence time of individual molecules, thereby increasing the probability of detecting single-molecule binding events. This innovative approach ensures consistent and reliable SERS single-molecule detection in complex mixtures, paving the way for advanced applications in biochemical sensing and diagnostics.

Length-flexible strategies for efficient SERS performance in gold-nanorod-gapped nanoantennas

Surface-enhanced Raman spectroscopy (SERS) using gold-nanorod-dimer nanoantennas has shown great potential in various applications. This reflects in their large values of the customary figure of merit of SERS: the enhancement factor (EF), which is essentially the fourth power of the electric field integrated at the gap, the location at which target molecules are to be sensed. However, fabrication errors in the nanorod lengths can lead to significant variations in the enhancement factor, resulting in performance limitations whenever low values of EF are encountered. Here, we report both design and procedural strategies to address this issue. First, we show that by reducing the nanorod diameter from 360 to 260 nm, the EF minima can be avoided for any nanorod length, mitigating the impact of fabrication errors. In addition, we explore the influence of incident wave polarization and orientation on the EF. Our simulations reveal that by tilting the excitation away from normal incidence, it is possible to substantially enhance EF under conditions that would otherwise exhibit low enhancement. In particular, this includes the case of 360 nm diameter. These findings expand the fabrication tolerance and broaden the range of usability of gold-nanorod-dimer nanoantennas, enabling more robust and reliable SERS performance. Importantly, we also show that these strategies also apply to nanoantennas with covered nanorod ends, which are of particular interest for realizing hybrid devices that combine SERS with electrical transport measurements.

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.

Insights of Surface-Enhanced Raman Spectroscopy Detection by Guiding Molecules into Nanostructures to Activate Hot Spots

A misunderstanding of how target molecules enter hot spot nanostructures has significantly hindered the advancement of surface-enhanced Raman spectroscopy (SERS) detection methods in recent years. The challenge lies in finding convenient ways to transport target molecules to various nanostructures. In this work, we discovered that filling the gaps in empty nanostructures with water is often difficult, as metal surfaces are not well wetted. Additionally, the adsorption of pollutants from the air reduces the water wettability within the nanogaps, severely restricting the diffusion of molecules in the hot spots. This study proposes a method that uses a binary solvent mixture of ethanol and water (EtOH-H2O) to effectively guide target molecules into the nanostructures containing numerous hot spots. By utilizing the tunable surface tension gradient of this binary solvent mixture, we can control solvent transport within the nanostructures, significantly enhancing the activity of the hot spots and increasing the efficiency of SERS detection. The detection limit of this simple and rapid binary solvent mixing method is improved by 2-3 orders of magnitude compared to traditional methods that use only water or ethanol as solvents while also demonstrating high reproducibility. This method can be widely applied to various nanostructures for different types of molecules, maximizing the efficient use of intrinsic hot spots. This innovative approach provides new momentum for the advancement of SERS technology and lays a solid foundation for its widespread adoption in various analytical applications.

Advances and applications of dynamic surface-enhanced Raman spectroscopy (SERS) for single molecule studies

Dynamic surface-enhanced Raman spectroscopy (SERS) is nowadays one of the most interesting applications of SERS, in particular for single molecule studies. In fact, it enables the study of real-time processes at the molecular level. This review summarizes the latest developments in dynamic SERS techniques and their applications, focusing on new instrumentation, data analysis methods, temporal resolution and sensitivity improvements, and novel substrates. We highlight the progress and applications of single-molecule dynamic SERS in monitoring chemical reactions, catalysis, biomolecular interactions, conformational dynamics, and real-time sensing and detection. We aim to provide a comprehensive review on its advancements, applications as well as its current challenges and development frontiers.

Recent Advances in DNA Origami-Enabled Optical Biosensors for Multi-Scenario Application

Over the past few years, significant progress has been made in DNA origami technology due to the unrivaled self-assembly properties of DNA molecules. As a highly programmable, addressable, and biocompatible nanomaterial, DNA origami has found widespread applications in biomedicine, such as cell scaffold construction, antimicrobial drug delivery, and supramolecular enzyme assembly. To expand the scope of DNA origami application scenarios, researchers have developed DNA origami structures capable of actively identifying and quantitatively reporting targets. Optical DNA origami biosensors are promising due to their fast-to-use, sensitive, and easy implementation. However, the conversion of DNA origami to optical biosensors is still in its infancy stage, and related strategies have not been systematically summarized, increasing the difficulty of guiding subsequent researchers. Therefore, this review focuses on the universal strategies that endow DNA origami with dynamic responsiveness from both de novo design and current DNA origami modification. Various applications of DNA origami biosensors are also discussed. Additionally, we highlight the advantages of DNA origami biosensors, which offer a single-molecule resolution and high signal-to-noise ratio as an alternative to traditional analytical techniques. We believe that over the next decade, researchers will continue to transform DNA origami into optical biosensors and explore their infinite possible uses.

Toward Precise Fabrication of Finite-Sized DNA Origami Superstructures

DNA origami enables the precise construction of 2D and 3D nanostructures with customizable shapes and the high-resolution organization of functional materials. However, the size of a single DNA origami is constrained by the length of the scaffold strand, and since its inception, scaling up the size and complexity has been a persistent pursuit. Hierarchical self-assembly of DNA origami units offers a feasible approach to overcome the limitation. Unlike periodic arrays, finite-sized DNA origami superstructures feature well-defined structural boundaries and uniform dimensions. In recent years, increasing attention has been directed toward precise control over the hierarchical self-assembly of DNA origami structures and their applications in fields such as nanophotonics, biophysics, and material science. This review summarizes the strategies for fabricating finite-sized DNA origami superstructures, including heterogeneous self-assembly, self-limited self-assembly, and templated self-assembly, along with a comparative analysis of the advantages and limitations of each approach. Subsequently, recent advancements in the application of these structures are discussed from a structure design perspective. Finally, an outlook on the current challenges and potential future directions is provided, highlighting opportunities for further research and development in this rapidly evolving field.

Highly Monodisperse Stable Gold Nanorod Powder for Optical Sensor

Gold nanorods (GNRs) as plasmonic metal nanoparticles are valuable for optical applications due to their tunable plasmonic properties. However, conventional colloidal GNRs face significant optical instability during storage, which limits their practical use. In this work, we developed a highly dispersible GNR powder using an octadecyl trimethylammonium bromide (C18TAB)-assisted freeze-drying method, preserving the optical and chemical sensing properties of GNRs for over 4 months. Compared with C16TAB, C18TAB significantly enhances the GNRs dispersibility even at lower concentrations. Our study demonstrates that C18TAB forms a sponge-like crystal structure that prevents aggregation during the freeze-drying process. The resulting GNR powder retains its plasmonic features and water dispersibility, achieving near-identical optical properties to those of fresh GNR solutions. This stability enabled creation of a liquid-free colorimetric test kit with a long shelf life. This work marks a significant step forward in the use of GNRs as standard analytical reagents, opening new avenues for real-world applications.

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.

Phase-Engineered Transition Metal Dichalcogenides for Highly Efficient Surface-Enhanced Raman Scattering

Phase engineering of two-dimensional (2D) transition metal dichalcogenides (TMDs) is an attractive avenue to construct new surface-enhanced Raman scattering (SERS) substrates. Herein, 2D WS2 and MoS2 monolayers with high-purity distorted octahedral phase (1T') are prepared for highly sensitive SERS detection of analytes (e.g., rhodamine 6G, rhodamine B and crystal violet). 1T'-WS2 and 1T'-MoS2 monolayers show the detection limits of 8.28 × 10-12 and 8.57 × 10-11 M for rhodamine 6G, with the enhancement factors of 4.6 × 108 and 3.9 × 107, respectively, which are comparable to noble-metal substrates, outperforming semiconducting 2H-W(Mo)S2 monolayers and most of the reported non-noble-metal substrates. First-principles density functional theory calculations show that their Raman enhancement effect is mainly ascribed to highly efficient interfacial charge transfer between the 1T'-W(Mo)S2 monolayers and analytes. Our study reveals that 2D TMDs with semimetallic 1T' phase are promising as next-generation SERS substrates.

Exploration of cucurbituril-mediated SERS plasmonic nanoarrays with sub-nanometer gaps

The uneven distribution of hotspots and the challenges associated with precise analyte localization within these hotspots present significant hurdles in the field of surface-enhanced Raman scattering (SERS). Here, at the water-oil interface, gold nanoparticles (AuNPs) interconnected by cucurbiturils[8] (CB[8]) with sub-nanometer gaps (AuNPs:CB[8]) were organized into plasmonic arrays. This arrangement was engineered to generate highly efficient hotspots. The CB[8] molecules, serving a dual role, not only facilitated the assembly of AuNPs with sub-nanometer (~ 1 nm) gaps to create intense plasmonic hotspots but also acted as molecular traps, enabling the precise localization of molecules within these hotspots. By comparing the enhancement effect of probe molecule on Au nanofilm, AuNPs:CB[8] colloids, and AuNPs:CB[8] nanofilm, it was found that the SERS intensity of the E1 characteristic peak in AuNPs:CB[8] nanofilm is five times higher than that on Au nanofilm, and more than 104 times higher than that of AuNPs:CB[8] colloids. The gaps are also accessible to different electronegativite molecules, such as estrone, p-aminoazobenzene, or methylene blue, which are captured at the plasmonic hotspots by the interaction of CB[8]. The method was employed for the practical detection of artificial antioxidant butylated hydroxyanisole (BHA), which has a weak Raman scattering cross-section, by coupling it with a reaction to enhance its SERS effect. The detection limit of BHA in soybean oil sample is 5.89 × 10-8 mol/L, with the recovery range 85.1-115%. In conclusion, this hot-spot design and molecular capture approach will offer a highly effective method for detecting weak Raman scattering cross-section molecules and holds great promise for practical applications in the future.

Charge Transfer Plasmons Enabled by Supramolecular Plug: From Optoelectronic Switching to Enhanced Chiral Sensing

Miniaturization and integration of plasmonic nanodevices are fundamentally limited by quantum tunneling, which leads to quantum plasmonics with reduced local E-field intensity. Despite significant efforts devoted to modeling and deterring the detrimental effect of quantum plasmonics, the modulation and application of electron transport through the subnanometer gaps seems rarely exploited due to the limited tunability of conventional quantum materials. Here, we establish a supramolecular plasmonic system made of pillar[5]arene complexes and plasmonic resonators (nanoparticle-on-mirror, NPoM). The supramolecular assemblies significantly enhance the gap conductance of NPoM, which results in a blue-shift of the coupled plasmons. Plasmonic hot-electron transport with laser excitation further modulates the gap plasmons, which are fully reversible and beneficial for enhanced chiroptic sensing. Such a conductive supramolecular plasmonic system not only suggests an optoelectronic switching strategy for charge transfer plasmons but also provides a superior sensing platform for single molecules.

A SERS-based point-of-care testing approach for efficient determination of diquat and paraquat residues using a flexible silver flower-coated melamine sponge

Diquat (DQ) and paraquat (PQ) residues in food are potential hazards to consumers' health. Point-of-care testing (POCT) of them remains challenging. Based on surface-enhanced Raman spectroscopy (SERS) technology, we developed a POCT strategy for DQ and PQ on apple surface and in apple juice. A point-of-use composite was fabricated using a piece of porous melamine sponge (MS) modified with silver nanoflowers (AgNFs), combining the specificity of the SERS fingerprint and the excellent adsorption capacity of MS. Using this dual-functional AgNFs@MS, the on-site determination of the DQ and PQ residues was completed within 3 min without pretreatment. Clear trends were observed between SERS intensity and logarithmic concentrations, with r values from 0.962 to 0.984. The limit of detection of DQ and PQ were 0.14-0.70 ppb in apple juice and on apple surface. This study provides a new point-of-use alternative for rapidly detecting DQ and PQ residues in nonlaboratory settings.

Recent Progress in the Synthesis of 3D Complex Plasmonic Intragap Nanostructures and Their Applications in Surface-Enhanced Raman Scattering

Plasmonic intragap nanostructures (PINs) have garnered intensive attention in Raman-related analysis due to their exceptional ability to enhance light-matter interactions. Although diverse synthetic strategies have been employed to create these nanostructures, the emphasis has largely been on PINs with simple configurations, which often fall short in achieving effective near-field focusing. Three-dimensional (3D) complex PINs, distinguished by their intricate networks of internal gaps and voids, are emerging as superior structures for effective light trapping. These structures facilitate the generation of hot spots and hot zones that are essential for enhanced near-field focusing. Nevertheless, the synthesis techniques for these complex structures and their specific impacts on near-field focusing are not well-documented. This review discusses the recent advancements in the synthesis of 3D complex PINs and their applications in surface-enhanced Raman scattering (SERS). We begin by describing the foundational methods for fabricating simple PINs, followed by a discussion on the rational design strategies aimed at developing 3D complex PINs with superior near-field focusing capabilities. We also evaluate the SERS performance of various 3D complex PINs, emphasizing their advanced sensing capabilities. Lastly, we explore the future perspective of 3D complex PINs in SERS applications.

Selenium-Doped Seeded Growth of Truncated Octahedral Gold Nanocrystals with Surface Concavities for Surface-Enhanced Raman Spectroscopy

Concave nanocrystals stand out as a testament to the importance of the nanoscale morphology in dictating the functional properties of materials. In this report, we introduce a facile synthesis method for producing gold (Au) nanocrystals with a truncated octahedral morphology that features surface concavities (Au CNTOs). The incorporation of selenium (Se) doping into the truncated octahedral Au seeds was essential for their enlargement and the formation of concave structures. By simply adjusting the quantity of seeds, we could control the size of the nanocrystals while maintaining their distinctive morphology and surface concavity. The formation mechanism suggests that Se doping likely passivates the side faces, thereby slowing growth and promoting atomic deposition at the edges and corners. The resulting Se-doped Au CNTOs exhibited strong localized surface plasmon resonance (LSPR) absorptions in the visible spectrum and the SERS performance of their assemblies was demonstrated through crystal violet detection, reaching enhancement factors around 105. This study presents an innovative approach to synthesizing concave Au nanocrystals through the incorporation of selenium during a seeded growth process, offering insights into the strategic design of plasmonic nanostructures.

DNA origami-templated gold nanorod dimer nanoantennas: enabling addressable optical hotspots for single cancer biomarker SERS detection

The convergence of DNA origami and surface-enhanced Raman spectroscopy (SERS) has opened a new avenue in bioanalytical sciences, particularly in the detection of single-molecule proteins. This breakthrough has enabled the development of advanced sensor technologies for diagnostics. DNA origami offers a highly controllable framework for the precise positioning of nanostructures, resulting in superior SERS signal amplification. In our investigation, we have successfully designed and synthesized DNA origami-based gold nanorod monomer and dimer assemblies. Moreover, we have evaluated the potential of dimer assemblies for label-free detection of a single biomolecule, namely epidermal growth factor receptor (EGFR), a crucial biomarker in cancer research. Our findings have revealed that the significant Raman amplification generated by DNA origami-assembled gold nanorod dimer nanoantennas facilitates the label-free identification of Raman peaks of single proteins, which is a prime aim in biomedical diagnostics. The present work represents a significant advancement in leveraging plasmonic nanoantennas to realize single protein SERS for the detection of various cancer biomarkers with single-molecule sensitivity.

Ultrasensitive Surface-Enhanced Raman Scattering Platform for Protein Detection via Active Delivery to Nanogaps as a Hotspot

Surface-enhanced Raman scattering (SERS) is an attractive technique in molecular detection with high sensitivity and label-free characteristics. However, its use in protein detection is limited by the large volume of proteins, hindering its approach to the narrow spaces of hotspots. In this study, we fabricated a Au nanoTriangle plate Array on Gel (AuTAG) as an SERS substrate by attaching a Au nanoTriangle plate (AuNT) arrangement on a thermoresponsive hydrogel surface. The AuTAG acts as an actively tunable plasmonic device, on which the interparticle distance is altered by controlling temperature via changes in hydrogel volume. Further, we designed a Gel Filter Trapping (GFT) method as an active protein delivery strategy based on the characteristics of hydrogels, which can absorb water and separate biopolymers through their three-dimensional (3D) polymer networks. On the AuTAGs, fabricated with AuNTs modified with charged surface ligands to prevent the nonspecific adsorption of analytes to particles, the GFT method helped the delivery of proteins to hotspot areas on the AuNT arrangement. This combination of a AuTAG substrate and the GFT method enables ultrahigh sensitivity for protein detection by SERS up to a single-molecule level as well as a wide quantification concentration range of 6 orders due to their geometric advantages.

Controllable Construction of Aptamer-Modified Fe3O4@SiO2-Au Core-Shell-Satellite Nanocomposites with Surface-Enhanced Raman Scattering and Photothermal Properties and Their Effective Capture, Detection, and Elimination of Staphylococcus aureus

The early monitoring and inactivation of bacteria are of crucial importance in preventing the further spread of foodborne pathogens. Staphylococcus aureus (S. aureus), a prototypical foodborne pathogen, is widely present in the natural environment and has the capability to trigger a range of diseases at low concentrations. In this work, we designed Fe3O4@SiO2-Au core-shell-satellite nanocomposites (NCs) modified with aptamer for efficient capture, high-sensitivity surface-enhanced Raman scattering (SERS) detection, and photothermal therapy (PTT) against S. aureus. Fe3O4@SiO2-Au NCs with tunable Au nanocrystal nanogaps were prepared. By combining the finite-difference time-domain (FDTD) method and experimental results, we studied the electric field distribution of Fe3O4@SiO2-Au under different Au nanogaps and ultimately obtained the optimal SERS substrate FSA-60. The modification of aptamer on the surfaces of FSA-60 could be used for the specific capture and selective detection of S. aureus, achieving a detection limit of as low as 50 cfu/mL. Furthermore, Apt-FSA-60 possessed excellent photothermal properties, demonstrating the strong photothermal killing ability against S. aureus. Therefore, Apt-FSA-60 is a promising high-sensitivity SERS substrate and efficient photothermal agent and is expected to be widely applied and promoted in future disease prevention and treatment.

Watching a Single Enzyme at Work Using Single-Molecule Surface-Enhanced Raman Scattering and DNA Origami-Based Plasmonic Antennas

The detection of a single-enzyme catalytic reaction by surfaced-enhanced Raman scattering (SERS) is presented by utilizing DNA origami-based plasmonic antennas. A single horseradish peroxidase (HRP) was accommodated on a DNA origami nanofork plasmonic antenna (DONA) containing gold nanoparticles, enabling the tracing of single-molecule SERS signals during the peroxide reduction reaction. This allows monitoring of the structure of a single enzymatic catalytic center and products under suitable liquid conditions. Herein, we demonstrate the chemical changes of HRP and the appearance of tetramethylbenzidine (TMB), which works as a hydrogen donor before and after the catalytic reaction. The results show that the iron in HRP adopts Fe4+ and low spin states with the introduction of H2O2, indicating compound-I formation. Density functional theory (DFT) calculations were performed for later catalytic steps to rationalize the experimental Raman/SERS spectra. The presented data provide several possibilities for tracking single biomolecules in situ during a chemical reaction and further developing plasmon-enhanced biocatalysis.

DNA-Based Conductors: From Materials Design to Ultra-Scaled Electronics

Photolithography has been the foundational fabrication paradigm in current high-performance electronics. However, due to the limitation in fabrication resolution, scaling beyond a 20-nm critical dimension for metal conductors presents a significant challenge for photolithography. Structural DNA nanotechnology emerges as a promising alternative to photolithography, allowing for the site-specific assembly of nano-materials at single-molecule resolution. Substantial progresses have been achieved in the ultra-scaled DNA-based conductors, exhibiting novel transport characteristics and small critical dimensions. This review highlights the structure-transport property relationship for various DNA-based conductors and their potential applications in quantum /semiconductor electronics, going beyond the conventional scope focusing mainly on the shape diversity of DNA-templated metals. Different material synthesis methods and their morphological impacts on the conductivities are discussed in detail, with particular emphasis on the conducting mechanisms, such as insulating, metallic conducting, quantum tunneling, and superconducting. Furthermore, the ionic gating effect of self-assembled DNA structures in electrolyte solutions is examined. This review also suggests potential solutions to address current challenges in DNA-based conductors, encouraging multi-disciplinary collaborations for the future development of this exciting area.

High-Throughput Single-Molecule Surface-Enhanced Raman Spectroscopic Profiling of Single-Amino Acid Substitutions in Peptides by a Gold Plasmonic Nanopore

Simultaneous detection and structural characterization of protein variants on a single platform are highly desirable but technically challenging. Herein, we present a single-molecule spectral system based on a gold plasmonic nanopore for analyzing two peptides and their single-point mutated variants. The gold plasmonic nanopore enabled the high-throughput acquisition of surface-enhanced Raman scattering (SERS) spectra at the single-molecule level by electrically driving analytes into hot spots. Furthermore, a statistical method based on Boolean operations was developed to extract prominent features from fluctuated single-molecule SERS spectra. The effects of the single-amino acid substitutions on both the intramolecular interactions and the peptide conformations were directly characterized by the nanopore system, and the results agreed with the predictions by AlphaFold2. This study highlights the mutual benefits of spectroscopy and nanopore technology, whereby the gold plasmonic nanopore offers a powerful tool for the structural analysis of single-molecule proteins.

Functionalized DNA Origami-Enabled Detection of Biomarkers

Biomarkers are crucial physiological and pathological indicators in the host. Over the years, numerous detection methods have been developed for biomarkers, given their significant potential in various biological and biomedical applications. Among these, the detection system based on functionalized DNA origami has emerged as a promising approach due to its precise control over sensing modules, enabling sensitive, specific, and programmable biomarker detection. We summarize the advancements in biomarker detection using functionalized DNA origami, focusing on strategies for DNA origami functionalization, mechanisms of biomarker recognition, and applications in disease diagnosis and monitoring. These applications are organized into sections based on the type of biomarkers - nucleic acids, proteins, small molecules, and ions - and concludes with a discussion on the advantages and challenges associated with using functionalized DNA origami systems for biomarker detection.

Universal Click-Chemistry Approach for the DNA Functionalization of Nanoparticles

Nanotechnology has revolutionized the fabrication of hybrid species with tailored functionalities. A milestone in this field is the deoxyribonucleic acid (DNA) conjugation of nanoparticles, introduced almost 30 years ago, which typically exploits the affinity between thiol groups and metallic surfaces. Over the last decades, developments in colloidal research have enabled the synthesis of an assortment of nonmetallic structures, such as high-index dielectric nanoparticles, with unique properties not previously accessible with traditional metallic nanoparticles. However, to stabilize, integrate, and provide further functionality to nonmetallic nanoparticles, reliable techniques for their functionalization with DNA will be crucial. Here, we combine well-established dibenzylcyclooctyne-azide click-chemistry with a simple freeze-thaw method to achieve the functionalization of silica and silicon nanoparticles, which form exceptionally stable colloids with a high DNA surface density of ∼0.2 molecules/nm2. Furthermore, we demonstrate that these functionalized colloids can be self-assembled into high-index dielectric dimers with a yield of over 50% via the use of DNA origami. Finally, we extend this method to functionalize other important nanomaterials, including oxides, polymers, core-shell, and metal nanostructures. Our results indicate that the method presented herein serves as a crucial complement to conventional thiol functionalization chemistry and thus greatly expands the toolbox of DNA-functionalized nanoparticles currently available.

DNA Origami Plasmonic Nanoantenna for Programmable Biosensing of Multiple Cytokines in Cancer Immunotherapy

Herein, we report a DNA origami plasmonic nanoantenna for the programmable surface-enhanced Raman scattering (SERS) detection of cytokine release syndrome (CRS)-associated cytokines (e.g., tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ)) in cancer immunotherapy. Typically, the nanoantenna was made of self-assembled DNA origami nanotubes (diameter: ∼19 nm; length: ∼90 nm) attached to a silver nanoparticle-modified silicon wafer (AgNP/Si). Each DNA origami nanotube contains one miniature gold nanorod (AuNR) inside (e.g., length: ∼35 nm; width: ∼7 nm). Intriguingly, TNF-α and IFN-γ logically regulate the opening of the nanotubes and the dissociation of the AuNRs from the origami structure upon binding to their corresponding aptamers. On this basis, we constructed a complete set of Boolean logic gates that read cytokine molecules as inputs and return changes in Raman signals as outputs. Significantly, we demonstrated that the presented system enables the quantification of TNF-α and IFN-γ in the serum of tumor-bearing mice receiving different types of immunotherapies (e.g., PD1/PD-L1 complex inhibitors and STING agonists). The sensing results are consistent with those of the ELISA. This strategy fills a gap in the use of DNA origami for the detection of multiple cytokines in real systems.

Macroscopic Superlattice Membranes Self-Assembled from Gold Nanobipyramids with Precisely Tunable Tip Arrangements for SERS

A persistent challenge in utilizing Au nanocrystals for surface-enhanced Raman spectroscopy (SERS) lies in achieving controllable superstructures that maximize SERS performance. Here, a novel strategy is proposed to enhance the SERS performance by precisely adjusting the tip arrangements of Au nanobipyramids (BPs) in two-dimensional (2D) superlattices (SLs). This is achieved through ligand-exchange of Au BPs, followed by liquid-air interfacial assembly, resulting in large-area, transferrable SL membranes. The key to controlling the arrangement of Au BPs in the SLs is the regulation of the amount of free ligands added during self-assembly, which allows for the precise formation of various configurations such as tilted SLs, tip-on-tip SLs, and tip-to-tip SLs. Among these configurations, tip-on-tip SLs exhibit the highest enhancement factor for SERS, reaching an impressive value of 1.95×108, with uniform and consistent SERS signals across a large area. The experimental findings are further corroborated by simulations using the finite element method. This study establishes an efficient method for engineering the microstructure of 2D SLs composed of Au BPs, highlighting the importance of fine-tuning the tip arrangements of Au BPs to regulate SERS performance.

Efficient Poly-Adenine-Tailed DNA Functionalization of Gold Nanorods for Tailored Nanostructure Assembly

Gold nanorods (AuNRs) with unique optical properties play a pivotal role in applications in plasmonic imaging, small molecule detection, and photothermal therapy. However, challenges in DNA functionalization of AuNRs hinder their full potential due to the presence of a dense cetyltrimethylammonium bromide (CTAB) bilayer, impeding close DNA contact. In this study, we introduced a convenient approach for the rapid assembly of polyadenine (polyA) tailed DNA on AuNRs with control of DNA density, rigidity, and valence. We explored the impact of DNA with designed properties on the construction of core-satellite structures by employing AuNRs as cores and spherical gold nanoparticles (AuNSs) as satellites. Density, rigidity, and valence are identified as crucial factors for efficient construction. Specifically, polyA-tailed DNA modulated DNA density and reduced spatial hindrance and electrostatic repulsion, thereby facilitating the construction. Enhancing the rigidity of DNA and incorporating multiple binding sites can further improve the efficiency.

DNA Origami-Based Letterpress Printing of Gold Nanostructures with Predesigned Morphologies

Creating customizable metallic nanostructures in a simple and controllable manner has been a long-standing goal in nanoscience. In this study, we use DNA origami as a letterpress printing plate and gold nanoparticles as ink to produce predesigned gold nanostructures. The letterpress plate is reusable, enabling the repetitive production of predesigned gold nanostructures. Furthermore, by modifying the DNA origami letterpress plate on magnetic beads, we can simplify the printing processes. We have successfully printed gold nanoparticle dimers, trimers, straight and quadrilateral tetramers, and other nanostructures. Our approach improves the flexibility and stability of metallic nanostructures, simplifying both their design and their operation. It promises universal applicability in the fabrication of metamaterials, biosensors, and surface plasma nanooptics.