Surface-enhanced Raman scattering plasmonic enhancement using DNA origami-based complex metallic nanostructures

Highly Ordered Nanoassemblies of Janus Spherocylindrical Nanoparticles Adhering to Lipid Vesicles

In recent years, there has been a heightened interest in the self-assembly of nanoparticles (NPs) that is mediated by their adsorption onto lipid membranes. The interplay between the adhesive energy of NPs on a lipid membrane and the membrane's curvature energy causes it to wrap around the NPs. This results in an interesting membrane curvature-mediated interaction, which can lead to the self-assembly of NPs on lipid membranes. Recent studies have demonstrated that Janus spherical NPs, which adhere to lipid vesicles, can self-assemble into well-ordered nanoclusters with various geometries, including a few Platonic solids. The present study explores the additional effect of geometric anisotropy on the self-assembly of Janus NPs on lipid vesicles. Specifically, the current study utilized extensive molecular dynamics simulations to investigate the arrangement of Janus spherocylindrical NPs on lipid vesicles. We found that the additional geometric anisotropy significantly expands the range of NPs' self-assemblies on lipid vesicles. The specific geometries of the resulting nanoclusters depend on several factors, including the number of Janus spherocylindrical NPs adhering to the vesicle and their aspect ratio. The lipid membrane-mediated self-assembly of NPs, demonstrated by this work, provides an alternative cost-effective route for fabricating highly engineered nanoclusters in three dimensions. Such structures, with the current wide range of material choices, have great potential for advanced applications, including biosensing, bioimaging, drug delivery, nanomechanics, and nanophotonics.

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

The label-free identification of individual proteins from liquid samples by surface-enhanced Raman scattering (SERS) spectroscopy is a highly desirable goal in biomedical diagnostics. However, the small Raman scattering cross-section of most (bio-)molecules requires a means to strongly amplify their Raman signal for successful measurement, especially for single molecules. This amplification can be achieved in a plasmonic hotspot that forms between two adjacent gold nanospheres. However, the small (≈1-2 nm) gaps typically required for single-molecule measurements are not accessible for most proteins. A useful strategy would thus involve dimer structures with gaps large enough to accommodate single proteins, whilst providing sufficient field enhancement for single-molecule SERS. Here, we report on using a DNA origami scaffold for tip-to-tip alignment of gold nanorods with an average gap size of 8 nm. The gaps are accessible to streptavidin and thrombin, which are captured at the plasmonic hotspot by specific anchoring sites on the origami template. The field enhancement achieved for the nanorod dimers is sufficient for single-protein SERS spectroscopy with sub-second integration times. This design for SERS probes composed of DNA origami with accessible hotspots promotes future use for single-molecule biodiagnostics in the near-infrared range.

Non-close-packed hexagonal self-assembly of Janus nanoparticles on planar membranes

The adhesion modes of an ensemble of spherical Janus nanoparticles on planar membranes are investigated through large-scale molecular dynamics simulations of a coarse-grained implicit-solvent model. We found that the Janus nanoparticles adhering to planar membranes exhibit a rich phase behavior that depends on their adhesion energy density and areal number density. In particular, effective repulsive membrane-curvature-mediated interactions between the Janus nanoparticles lead to their self-assembly into an ordered hexagonal superlattice at intermediate densities and intermediate to high adhesion energy density, with a lattice constant determined by their areal density. The melting behavior of the hexagonal superlattice proceeds through a two-stage melting scenario in agreement with the Kosterlitz-Thouless-Halperin-Nelson-Young classical theory of two-dimensional melting.

Single-Step Plasmonic Dimer Printing by Gold Nanorod Splitting with Light

Optical printing is a flexible strategy to precisely pattern plasmonic nanoparticles for the realization of nanophotonic devices. However, the generation of strongly coupled plasmonic dimers by sequential particle printing can be a challenge. Here, we report an approach to generate and pattern dimer nanoantennas in a single step by optical splitting of individual gold nanorods with laser light. We show that the two particles that constitute the dimer can be separated by sub-nanometer distances. The nanorod splitting process is explained by a combination of plasmonic heating, surface tension, optical forces, and inhomogeneous hydrodynamic pressure introduced by a focused laser beam. This realization of optical dimer formation and printing from a single nanorod provides a means for dimer patterning with high accuracy for nanophotonic applications.

Lipid vesicles induced ordered nanoassemblies of Janus nanoparticles

Since many advanced applications require specific assemblies of nanoparticles (NPs), considerable efforts have been made to fabricate nanoassemblies with specific geometries. Although nanoassemblies can be fabricated through top-down approaches, recent advances show that intricate nanoassemblies can also be obtained through self-assembly, mediated for example by DNA strands. Here, we show, through extensive molecular dynamics simulations, that highly ordered self-assemblies of NPs can be mediated by their adhesion to lipid vesicles (LVs). Specifically, Janus NPs are considered so that the amount by which they are wrapped by the LV is controlled. The specific geometry of the nanoassembly is the result of effective curvature-mediated repulsion between the NPs and the number of NPs adhering to the LV. The NPs are arranged on the LV into polyhedra which satisfy the upper limit of Euler's polyhedral formula, including several deltahedra and three Platonic solids, corresponding to the tetrahedron, octahedron, and icosahedron.

DNA Self-Assembly of Single Molecules with Deterministic Position and Orientation

An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control, and well-defined orientation. The DNA origami technique has evolved into a highly versatile bottom-up nanofabrication methodology that fulfils almost all of these features. It enables the nanometric positioning of molecules and nanoparticles with stoichiometric control, and even the orientation of asymmetrical nanoparticles along predefined directions. However, orienting individual molecules has been a standing challenge. Here, we show how single molecules, namely, Cy5 and Cy3 fluorophores, can be incorporated in a DNA origami with controlled orientation by doubly linking them to oligonucleotide strands that are hybridized while leaving unpaired bases in the scaffold. Increasing the number of bases unpaired induces a stretching of the fluorophore linkers, reducing its mobility freedom, and leaves more space for the fluorophore to accommodate and find different sites for interaction with the DNA. Particularly, we explore the effects of leaving 0, 2, 4, 6, and 8 bases unpaired and find extreme orientations for 0 and 8 unpaired bases, corresponding to the molecules being perpendicular and parallel to the DNA double-helix, respectively. We foresee that these results will expand the application field of DNA origami toward the fabrication of nanodevices involving a wide range of orientation-dependent molecular interactions, such as energy transfer, intermolecular electron transport, catalysis, exciton delocalization, or the electromagnetic coupling of a molecule to specific resonant nanoantenna modes.

Recent developments in the use of gold and silver nanoparticles in biomedicine

Gold and silver nanoparticles (NPs) are widely used in the biomedical research both in the therapeutic and the sensing/diagnostics fronts. Both metals share some common optical properties with surface plasmon resonance being the most widely exploited property in therapeutics and diagnostics. Au NPs exhibit excellent light‐to‐heat conversion efficiencies and hence have found applications primarily in precision oncology, while Ag NPs have excellent antibacterial properties which can be harnessed in biomaterials' design. Both metals constitute excellent biosensing platforms owing to their plasmonic properties and are now routinely used in various optical platforms. The utilization of Au and Ag NPs in the COVID‐19 pandemic was rapidly expanded mostly in biosensing and point‐of‐care platforms and to some extent in therapeutics. In this review article, the main physicochemical properties of Au and Ag NPs are discussed with selective examples from the recent literature.

This article is categorized under:

Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease

Diagnostic Tools > In Vitro Nanoparticle‐Based Sensing

Nanotechnology Approaches to Biology > Nanoscale Systems in Biology

Rapid Exchange of Stably Bound Protein and DNA Cargo on a DNA Origami Receptor

Biomolecular complexes can form stable assemblies yet can also rapidly exchange their subunits to adapt to environmental changes. Simultaneously allowing for both stability and rapid exchange expands the functional capacity of biomolecular machines and enables continuous function while navigating a complex molecular world. Inspired by biology, we design and synthesize a DNA origami receptor that exploits multivalent interactions to form stable complexes that are also capable of rapid subunit exchange. The system utilizes a mechanism first outlined in the context of the DNA replisome, known as multisite competitive exchange, and achieves a large separation of time scales between spontaneous subunit dissociation, which requires days, and rapid subunit exchange, which occurs in minutes. In addition, we use the DNA origami receptor to demonstrate stable interactions with rapid exchange of both DNA and protein subunits, thus highlighting the applicability of our approach to arbitrary molecular cargo, an important distinction with canonical toehold exchange between single-stranded DNA. We expect this study to benefit future studies that use DNA origami structures to exploit multivalent interactions for the design and synthesis of a wide range of possible kinetic behaviors.

DNA-mediated hierarchical organization of gold nanoprisms into 3D aggregates and their application in surface-enhanced Raman scattering

Colloidal crystallization using DNA provides a robust method for fabricating highly programmable nanoparticle superstructures with collective plasmonic properties. Here, we report on the DNA-guided fabrication of 3D plasmonic aggregates from polydisperse gold nanoprisms. We first construct 1D crystals via DNA-induced and shape-directed face-to-face assembly of anisotropic gold nanoprisms. Using the near-T_m thermal annealing approach that promotes long-range DNA-induced interaction and ordering, we then assemble 1D nanoprism crystals into a 3D nanoprism aggregate that exhibits a polycrystalline morphology with nanoscale ordering and microscale dimensions. The presence of closely packed nanoprism arrays over a large area gives rise to strong near-field plasmonic coupling and generates a high density of plasmonic hot spots within the 3D nanoprism aggregates that exhibit excellent surface-enhanced Raman scattering performance. The plasmonic 3D nanoprism aggregates demonstrate significant SERS enhancement (<10⁶), and low detection limits (10^-9M) with good sample-to-sample reproducibility (CV ∼ only 5.6%) for SERS analysis of the probe molecule, methylene blue. These findings highlight the potential of 3D anisotropic nanoparticle aggregates as functional plasmonic nanoarchitectures that could find applications in sensing, photonics, optoelectronics and lasing.

SERS substrate fabrication for biochemical sensing: towards point-of-care diagnostics

Rapid technology development and economic growth have brought attention to public health issues, such as food safety and environmental pollution, which creates an ever-increasing demand for fast and portable sensing technologies. Portable surface-enhanced Raman spectroscopy (SERS) capable of various analyte detection with low concentration in a convenient manner shows advantages in sensing technology including enhanced diagnostic precision, improved diagnostic efficiency, reduced diagnostic cost, and alleviation of patient pain, which emerges as a promising candidate for point-of-care testing (POCT). SERS detection technology based on different nanostructures made of noble metal-based nanomaterials can increase the sensitivity of Raman scattering by 6-8 orders of magnitude, making Raman based trace detection possible, and greatly promote the application scenarios of portable Raman spectrometers. In this perspective, we provide an overview of fundamental knowledge about the SERS mechanism including chemical and electromagnetic field enhancement mechanisms, the design and fabrication of SERS substrates based on materials, progress of using SERS for POCT in biochemical sensing and its clinical applications. Furthermore, we present the prospective of developing new nanomaterials with different functionalities for advanced SERS substrates, as well as the future advancement of biomedical sensing and clinical potential of SERS technology.

A Versatile DNA Origami-Based Plasmonic Nanoantenna for Label-Free Single-Molecule Surface-Enhanced Raman Spectroscopy

DNA origami technology allows for the precise nanoscale assembly of chemical entities that give rise to sophisticated functional materials. We have created a versatile DNA origami nanofork antenna (DONA) by assembling Au or Ag nanoparticle dimers with different gap sizes down to 1.17 nm, enabling signal enhancements in surface-enhanced Raman scattering (SERS) of up to 10¹¹. This allows for single-molecule SERS measurements, which can even be performed with larger gap sizes to accommodate differently sized molecules, at various excitation wavelengths. A general scheme is presented to place single analyte molecules into the SERS hot spots using the DNA origami structure exploiting covalent and noncovalent coupling schemes. By using Au and Ag dimers, single-molecule SERS measurements of three dyes and cytochrome c and horseradish peroxidase proteins are demonstrated even under nonresonant excitation conditions, thus providing long photostability during time-series measurement and enabling optical monitoring of single molecules.

DNA origami: an outstanding platform for functions in nanophotonics and cancer therapy

Due to the proposal and evolution of the DNA origami technique over the past decade, DNA molecules have been utilized as building blocks for the precise construction of nanoscale architectures. Benefiting from the superior programmability of DNA molecules, the sequence-dependent recognition mechanism and robust complementation among DNA strands make it possible to customize almost arbitrary structures. Such an assembly strategy bypasses some of the limits of conventional fabrication methods; the fabrication accuracy and complexity of the target product are unprecedentedly promoted as well. Furthermore, due to the spatial addressability of the final products, nanostructures assembled through the DNA origami technique can also serve as a versatile platform for the spatial positioning of functional elements, represented by colloidal nanoparticles (NPs). The subsequent fabrication of heterogeneous functional nanoarchitectures is realized via modifying colloidal NPs with DNA strands and manipulating them to anchor into DNA origami templates. This has given rise to investigations of their novel properties in nanophotonics and therapeutic effects towards some diseases. In this review, we survey the crucial progress in the development of DNA origami design, assembly and structural analysis and summarize available applications in nanophotonics and cancer therapy based on the object-dressed DNA origami complex. Moreover, we elucidate the development of this field and discuss the potential directions of this kind of application-oriented nanomanufacturing.

3D DNA Nanostructures: The Nanoscale Architect

Structural DNA nanotechnology is a pioneering biotechnology that presents the opportunity to engineer DNA-based hardware that will mediate a profound interface to the nanoscale. To date, an enormous library of shaped 3D DNA nanostructures have been designed and assembled. Moreover, recent research has demonstrated DNA nanostructures that are not only static but can exhibit specific dynamic motion. DNA nanostructures have thus garnered significant research interest as a template for pursuing shape and motion-dependent nanoscale phenomena. Potential applications have been explored in many interdisciplinary areas spanning medicine, biosensing, nanofabrication, plasmonics, single-molecule chemistry, and facilitating biophysical studies. In this review, we begin with a brief overview of general and versatile design techniques for 3D DNA nanostructures as well as some techniques and studies that have focused on improving the stability of DNA nanostructures in diverse environments, which is pivotal for its reliable utilization in downstream applications. Our main focus will be to compile a wide body of existing research on applications of 3D DNA nanostructures that demonstrably rely on the versatility of their mechanical design. Furthermore, we frame reviewed applications into three primary categories, namely encapsulation, surface templating, and nanomechanics, that we propose to be archetypal shape- or motion-related functions of DNA nanostructures found in nanoscience applications. Our intent is to identify core concepts that may define and motivate specific directions of progress in this field as we conclude the review with some perspectives on the future.

A Programmable DNA-Silicification-Based Nanocavity for Single-Molecule Plasmonic Sensing

Plasmonic nanocavities are highly desirable for optical sensing because of their singular ability to confine light into deep subwavelength volumes. Yet, it remains profoundly challenging to fabricate structurally resilient nanocavities with high fidelity, and to obtain direct, noninvasive visualization of the plasmonic hotspots within such constructs. Herein, highly precise and robust nanocavities, entitled DNA-silicified template for Raman optical beacon (DNA-STROBE), are engineered by using silicified DNA scaffolds for spatial organization of discrete plasmonic nanoparticles. In addition to substantially enhancing structural stability and chemical inertness, DNA silicification significantly improves nanogap control, resulting simultaneously in large and controlled local electromagnetic field enhancement. The ultrasmall mode volume of the DNA-STROBE constructs promotes single-molecule occupancy enabling surface-enhanced Raman spectroscopy (SERS) observations of single-molecule activity even at elevated background concentration, significantly relaxing the restrictive pico- to nanomolar molecular concentration condition typically required for such investigations. Additionally, leveraging super-resolution SERS measurements allows noninvasive and diffraction-unlimited spatial profiling of otherwise unresolvable plasmonic hotspots. The highly programmable and reproducible nature of the DNA-STROBE, coupled with its quantitative label-free molecular readouts, provides a versatile platform with applications across the spectrum of nanophotonics and biomedical sciences.

DNA-induced assembly of gold nanoprisms and polystyrene beads into 3D plasmonic SERS substrates

The utilization of nanoparticle-polymer bead hybrid nanostructures as a SERS substrate depends on the control of the deposition, density, and distribution of nanoparticles on the bead surface. Here we demonstrate the fabrication of a large area SERS substate via a two- step DNA mediated assembly of gold nanoprisms and polystyrene (PS) beads into a large ensemble of beads that are densely coated with nanoprisms. First, nanoprisms are loaded on PS beads through DNA hybridization. The close packed arrangement of anisotropic nanoprisms in different orientations on a bead surface results in a plasmonic substrate with a variable nanogap size ranging 1-20 nm. Nanoprisms-coated beads are then assembled into a large stack or aggregate of beads using a DNA-induced crystallization approach. Each aggregate consists of 20-50 nanoprisms-coated beads, leading to the formation a large area of three-dimensional SERS substrate with a high-density of hot spots for SERS enhancement. An excellent enhancement factor (EF) of [Formula: see text] and a very high detection sensitivity (up to 10^-10 M) are observed for the analysis of a probe molecule (Methylene blue) using the SERS substrate.

Fabrication and SERS properties of complex and organized nanoparticle plasmonic clusters stable in solution

SERS activity can be increased by the formation of hot spots at the interparticle junctions of plasmonic nanoparticles in very close proximity, dramatically improving the enhancement factors in comparison with isolated nanoparticles. Controlling the number and geometrical architecture of hot spots, while endowing the clusters with colloidal stability, results in feasible optical sensors, able to provide quantitative SERS responses. Here, we review the approaches proposed to date to produce colloidal stable clusters, focusing on the control of the coordination number of nanoparticle assemblies and interparticle gaps. Clusters of spherical nanoparticles of the same size and rods of the same size are described to subsequently outline core-satellite constructs of nanoparticles of different sizes. Besides, purification processes for nanoparticle clusters are revised to provide efficient production in high yields.

Design and synthesis of pleated DNA origami nanotubes with adjustable diameters

DNA origami allows for the synthesis of nanoscale structures and machines with nanometre precision and high yields. Tubular DNA origami nanostructures are particularly useful because their geometry facilitates a variety of applications including nanoparticle encapsulation, the construction of artificial membrane pores and as structural scaffolds that can uniquely spatially arrange nanoparticles in circular, linear and helical arrays. Here we report a system of parametrization for the design of radially symmetric DNA origami nanotubes with adjustable diameter, length, crossover density, pleat angle and chirality. The system is implemented into a computational algorithm that provides a practical means to navigate the complex geometry of DNA origami nanotube design. We apply this in the design, synthesis and characterization of novel DNA origami nanotubes. These include structures with pleated walls where the same number of duplexes can form nanotubes with different diameters, and to vary the diameter within the same structure. We also construct nanotubes that can be reconfigured into different chiral shapes. Finally, we explore the effect of strain on the local and global geometry of DNA origami nanotubes and demonstrate how pleated walls can provide a strategy to rigidify nanotubes and to construct closely packed parallel duplexes.

Programming Surface-Enhanced Raman Scattering of DNA Origami-templated Metamolecules

DNA origami holds an unprecedented capability on assembling metallic nanoparticles into designer plasmonic metamolecules of emerging properties, including surface-enhanced Raman scattering (SERS). SERS metamolecules were produced by positioning nanoparticles in close proximity to each other on a DNA origami template for Raman enhancement. In earlier reports, SERS metamolecules were generally assembled into clusters containing small number of nanoparticles (2, 3, or 4) and thus had limited programmability over SERS. Herein, we expanded the structural complexity of SERS metamolecules by increasing the number of nanoparticles and by arranging them into sophisticated configurations. DNA origami hexagon tile was used as the assembling template to fabricate clusters consisting of 6, 7, 12, 18, and 30+ metallic nanoparticles. Programmable SERS was realized via controlling the size, number, or spatial arrangement of nanoparticles. We believe this method offers a general platform for fabricating sophisticated nanodevices with programmable SERS that may be applied to a variety of fields including plasmonics, nanophotonics, and sensing.

DNA Origami as Emerging Technology for the Engineering of Fluorescent and Plasmonic-Based Biosensors

DNA nanotechnology is a powerful and promising tool for the development of nanoscale devices for numerous and diverse applications. One of the greatest potential fields of application for DNA nanotechnology is in biomedicine, in particular biosensing. Thanks to the control over their size, shape, and fabrication, DNA origami represents a unique opportunity to assemble dynamic and complex devices with precise and predictable structural characteristics. Combined with the addressability and flexibility of the chemistry for DNA functionalization, DNA origami allows the precise design of sensors capable of detecting a large range of different targets, encompassing RNA, DNA, proteins, small molecules, or changes in physico-chemical parameters, that could serve as diagnostic tools. Here, we review some recent, salient developments in DNA origami-based sensors centered on optical detection methods (readout) with a special emphasis on the sensitivity, the selectivity, and response time. We also discuss challenges that still need to be addressed before this approach can be translated into robust diagnostic devices for bio-medical applications.

DNA-Modulated Plasmon Resonance: Methods and Optical Applications

The near-field effects in the vicinity of metallic nanoparticle surfaces, as induced by electromagnetic radiation with specific wavelength, give rise to a variety of novel optical properties and attractive applications because of surface plasmons, which are the coherent oscillations of conduction electrons on a metal surface. The interdisciplinary field of plasmonics has witnessed vigorous growth, promoting research on the modulation of plasmon resonance by constructing advanced plasmonic nanoarchitectures with controllable size, morphology, or interparticle coupling. Among diversified tools, deoxyribonucleic nucleic acid (DNA) possesses prominent superiority as a result of its designability, programmability, addressability, and ease of nanomaterial modification. In this review, we focus on the methods and optical applications of plasmon resonance modulation accomplished by DNA nanotechnology. Recent developments in the construction of DNA-mediated plasmonic nanoarchitecture and key ongoing research directions utilizing unique optical features are highlighted. Obstacles and challenges in this field are pointed out, followed by preliminary suggestions on some areas of opportunity that deserve attention.

Assembling PVP-Au NPs as portable chip for sensitive detection of cyanide with surface-enhanced Raman spectroscopy

Cyanide (C≡N) can lead to blood, cardiovascular system, and nervous system disorders owing to the acute and chronic toxicity; thus, aiming at the group or individual poisoning incidents, it is necessary to develop the sensitive and credible method for rapid on-site detection of poisons cyanide. Surface-enhanced Raman spectroscopy (SERS) with the advantages of providing fingerprint information of target molecules and single-molecules sensitivity has been widely used in on-site analysis; however, the SERS measurements always suffer from the problem of the stability of substrates. Here, the polyvinylpyrrolidone (PVP)-stabilized Au NPs (PVP-Au NPs) have been assembled through the simple, convenient evaporation-induced strategy with the large-scale hotspots substrates. The presence of PVP can not only facilitate the assembly of Au NPs but also prevent the corrosion of CN^- towards the Au NPs with the formation of [Au (CN)₂]^-1, providing high stable and reproducible SERS signals. Moreover, the PVP-Au NPs have been assembled on the Si wafer to fabricate the portable SERS chip for rapid on-site detection of CN^- with an RSD of 5.8% and limitation of 100 ppb. Furthermore, by coupling a portable Raman spectrometer, the SERS spectra of CN^- spiked into different specimens to simulate the poison samples have been collected and analyzed on SERS chips with the recovery of 89-103% and RSD not higher than 11.3%. Consequently, the fabricated SERS chip with assembled PVP-Au NPs can provide sensitive and credible detection for CN^- in different specimens, and then would satisfy the rapid on-site evaluation of CN^- in poisoning incidents with the portable Raman spectrometer. Graphical Abstract.

Charge Transfer-Mediated Blue Luminescence in Plasmonic Ag-Cu2O Quantum Nanoheterostructures

Metal-semiconductor hybrid nanoheterostructures have the possibility to exhibit new synergic properties other than the combination of properties from discrete components due to the interaction of metal and semiconductor components at the interfaces. Here, we have synthesized Ag-Cu₂O eyeball-shaped quantum nanoheterostructures with diameter ranging between 8 and 12 nm using a single-step low-cost solvothermal process. It is observed that the presence of a minimum 3% of Ag is required for the formation of Ag-Cu₂O quantum nanoheterostructures. The formation of nanoheterostructures has introduced new synergic properties like intense blue luminescence and surface-enhanced Raman scattering due to the interactions between Ag and Cu₂O atoms at the interfaces. The significant presence of charge transfer through the interfaces is identified from the peak shift of Raman modes. The increase in the electron density at the metal surface due to the charge transfer and the recombination of these electrons with sp- or d-band holes of Ag could be the effective mechanism of the observed blue luminescence. The blue luminescence of Ag-Cu₂O quantum nanoheterostructures together with its low band gap value (≈2.3 eV) is believed to have important applications in optoelectronic devices.

Glycerol-Assisted Construction of Long-Life Three-Dimensional Surface-Enhanced Raman Scattering Hot Spot Matrix

An evaporative self-assembly strategy for constructing a long-life 3D surface-enhanced Raman scattering (SERS) hot spot matrix is proposed with the assistance of glycerol to improve the spectral sensitivity and reproducibility. Different from the traditional wetting-state or drying-state methods, silver nanoparticles (AgNPs) in the glycerol-stabilized 3D SERS hot spot matrix can be maintained in the translation state for more than 7 days with the maximal uniformity of the interparticle distance. Brownian dynamics simulations reveal that more hot spots emerge in the glycerol-stabilized AgNPs matrix, and the distances between the AgNPs are not fixed but balanced in a small range by the interplay of the van der Waals attraction and the electrostatic repulsion. A 2 orders of magnitude extra SERS enhancement, more stable peak frequencies, and a narrower peak full width at half-maximum (fwhm) can therefore be obtained, which ensure extremely stable and reproducible SERS signals. Single-molecule detection sensitivity utilizing the glycerol-stabilized 3D SERS hot spot matrix has been demonstrated by collecting the SERS spectra of dye molecules at a concentration of as low as 0.5 aM (5 × 10^-19 M) with a good signal-to-noise ratio. A long lifetime, ultrahigh SERS enhancement, and extremely stable peak shape make the 3D SERS hot spot matrix a sensitive, practical, and reliable tool for the detection and analysis of analytes at ultralow concentration or even at the single-molecule level in complex matrixes.

Engineering State-of-the-Art Plasmonic Nanomaterials for SERS-Based Clinical Liquid Biopsy Applications

Precision oncology, defined as the use of the molecular understanding of cancer to implement personalized patient treatment, is currently at the heart of revolutionizing oncology practice. Due to the need for repeated molecular tumor analyses in facilitating precision oncology, liquid biopsies, which involve the detection of noninvasive cancer biomarkers in circulation, may be a critical key. Yet, existing liquid biopsy analysis technologies are still undergoing an evolution to address the challenges of analyzing trace quantities of circulating tumor biomarkers reliably and cost effectively. Consequently, the recent emergence of cutting-edge plasmonic nanomaterials represents a paradigm shift in harnessing the unique merits of surface-enhanced Raman scattering (SERS) biosensing platforms for clinical liquid biopsy applications. Herein, an expansive review on the design/synthesis of a new generation of diverse plasmonic nanomaterials, and an updated evaluation of their demonstrated SERS-based uses in liquid biopsies, such as circulating tumor cells, tumor-derived extracellular vesicles, as well as circulating cancer proteins, and tumor nucleic acids is presented. Existing challenges impeding the clinical translation of plasmonic nanomaterials for SERS-based liquid biopsy applications are also identified, and outlooks and insights into advancing this rapidly growing field for practical patient use are provided.

Quantizing single-molecule surface-enhanced Raman scattering with DNA origami metamolecules

Tailored metal nanoclusters have been actively developed to manipulate light at the subwavelength scale for nanophotonic applications. Nevertheless, precise arrangement of molecules in a hot spot with fixed numbers and positions remains challenging. Here, we show that DNA origami metamolecules with Fano resonances (DMFR) can precisely localize single dye molecules and produce quantified surface-enhanced Raman scattering (SERS) responses. To enable tailored plasmonic permutations, we develop a general and programmable method for anchoring a set of large gold nanoparticles (L-AuNPs) on prescribed n-tuple docking sites of super-origami DNA frameworks. A tetrameric nanocluster with four spatially organized 80-nm L-AuNPs exhibits peak-and-dip Fano characteristics. The drastic enhancement at the wavelength of the Fano minimum allows the collection of prominent SERS spectrum for even a single dye molecule. We expect that DMFR provides physical insights into single-molecule SERS and opens new opportunities for developing plasmonic nanodevices for ultrasensitive sensing, nanocircuits, and nanophotonic lasers.

Preparation of a Novel Raman Probe and Its Application in the Detection of Circulating Tumor Cells and Exosomes

The Raman probe plays an essential role in sensitive surface-enhanced Raman scattering (SERS) assay. Here, a novel Raman probe was developed by assembling gold nanoparticles in triangular pyramid DNA (TP-Au NPs). Such probe with intense electromagnetic hot spots can provide dramatically enhanced Raman scattering. Through assembling recognition DNA on one corner of the TP-DNA, the recognition event is definite and designable. The probe was characterized through TEM, and its SERS superiority was investigated. As models, circulating tumor cells and exosomes were detected with high sensitivity and selectivity by using this probe. Meanwhile, the developed SERS probe can also perform well in real world samples.

Amorphous Carbon Generation as a Photocatalytic Reaction on DNA-Assembled Gold and Silver Nanostructures

Background signals from in situ-formed amorphous carbon, despite not being fully understood, are known to be a common issue in few-molecule surface-enhanced Raman scattering (SERS). Here, discrete gold and silver nanoparticle aggregates assembled by DNA origami were used to study the conditions for the formation of amorphous carbon during SERS measurements. Gold and silver dimers were exposed to laser light of varied power densities and wavelengths. Amorphous carbon prevalently formed on silver aggregates and at high power densities. Time-resolved measurements enabled us to follow the formation of amorphous carbon. Silver nanolenses consisting of three differently-sized silver nanoparticles were used to follow the generation of amorphous carbon at the single-nanostructure level. This allowed observation of the many sharp peaks that constitute the broad amorphous carbon signal found in ensemble measurements. In conclusion, we highlight strategies to prevent amorphous carbon formation, especially for DNA-assembled SERS substrates.

Create Nanoscale Patterns with DNA Origami

Structural deoxyribonucleic acid (DNA) nanotechnology offers a robust platform for diverse nanoscale shapes that can be used in various applications. Among a wide variety of DNA assembly strategies, DNA origami is the most robust one in constructing custom nanoshapes and exquisite patterns. In this account, the static structural and functional patterns assembled on DNA origami are reviewed, as well as the reconfigurable assembled architectures regulated through dynamic DNA nanotechnology. The fast progress of dynamic DNA origami nanotechnology facilitates the construction of reconfigurable patterns, which can further be used in many applications such as optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.

DNA-Mediated Self-Assembly of Plasmonic Antennas with a Single Quantum Dot in the Hot Spot

DNA self-assembly is a powerful tool to arrange optically active components with high accuracy in a large parallel manner. A facile approach to assemble plasmonic antennas consisting of two metallic nanoparticles (40 nm) with a single colloidal quantum dot positioned at the hot spot is presented here. The design approach is based on DNA complementarity, stoichiometry, and steric hindrance principles. Since no intermediate molecules other than short DNA strands are required, the structures possess a very small gap (≈ 5 nm) which is desired to achieve high Purcell factors and plasmonic enhancement. As a proof-of-concept, the fluorescence emission from antennas assembled with both conventional and ultrasmooth spherical gold particles is measured. An increase in fluorescence is obtained, up to ≈30-fold, compared to quantum dots without antenna.

Highly Localized SERS Measurements Using Single Silicon Nanowires Decorated with DNA Origami-Based SERS Probe

Surface enhanced Raman spectroscopy (SERS) measurements are conventionally performed using assemblies of metal nanostructures on a macro- to micro-sized substrate or by dispersing colloidal metal nanoparticles directly onto the sample of interest. Despite intense use, these methods allow neither the removal of the nanoparticles after a measurement nor a defined confinement of the SERS measurement position. So far, tip enhanced Raman spectroscopy is still the key technique in this regard but not adequate for various samples mainly due to diminished signal enhancement compared to other techniques, poor device fabrication reproducibility, and cumbersome experimental setup requirements. Here, we demonstrate that a rational combination of only four gold nanoparticles (AuNPs) on a DNA origami template, and single silicon nanowires (SiNWs) yield functional optical amplifier nanoprobes for SERS. These nanoscale SERS devices offer a spatial resolution below the diffraction limit of light and still a high electric field intensity enhancement factor ( EF) of about 10⁵ despite of miniaturization.

Superficial-Layer-Enhanced Raman Scattering (SLERS) for Depth Detection of Noncontact Molecules

Although the strength of Raman signals can be increased by many orders of magnitude on noble metal nanoparticles, this enhancement is confined to an extremely short distance from the Raman-active surface. The key to the development of Raman spectroscopy for applications in diagnosis and detection of cancer and inflammatory diseases, and in pharmacology, relies on the capability of detecting analytes that are noninteractive with Raman-active surfaces. Here, a new Raman enhancement system is constructed, superficial-layer-enhanced Raman scattering (SLERS), by covering elongated tetrahexahedral gold nanoparticle arrays with a superficial perovskite (CH₃ NH₃ PbBr₃ ) film. Plasmonic decay is depressed along the vertical direction away from the noble metal surface and the penetration depth is increased in the perovskite media. The vertical penetration of SLERS is verified by the spatial distribution of the analytes via Raman imaging in layer-scanning mode.

DNA Origami Nanophotonics and Plasmonics at Interfaces

DNA nanotechnology provides a versatile toolbox for creating custom and accurate shapes that can serve as versatile templates for nanopatterning. These DNA templates can be used as molecular-scale precision tools in, for example, biosensing, nanometrology, and super-resolution imaging, and biocompatible scaffolds for arranging other nano-objects, for example, for drug delivery applications and molecular electronics. Recently, increasing attention has been paid to their potent use in nanophotonics since these modular templates allow a wide range of plasmonic and photonic ensembles ranging from DNA-directed nanoparticle and fluorophore arrays to entirely metallic nanostructures. This Feature Article focuses on the DNA-origami-based nanophotonics and plasmonics-especially on the methods that take advantage of various substrates and interfaces for the foreseen applications.

DNA-Assisted Assembly of Gold Nanostructures and Their Induced Optical Properties

Gold nanocrystals have attracted considerable attention due to their excellent physical and chemical properties and their extensive applications in plasmonics, spectroscopy, biological detection, and nanoelectronics. Gold nanoparticles are able to be readily modified and arranged with DNA materials and protein molecules, as well as viruses. Particularly DNA materials with the advantages endowed by programmability, stability, specificity, and the capability to adapt to functionalization, have become the most promising candidates that are widely utilized for building plenty of discrete gold nanoarchitectures. This review highlights recent advances on the DNA-based assembly of gold nanostructures and especially emphasizes their resulted superior optical properties and principles, including plasmonic extinction, plasmonic chirality, surface enhanced fluorescence (SEF), and surface-enhanced Raman scattering (SERS).

Dynamic Plasmonic System That Responds to Thermal and Aptamer-Target Regulations

The DNA origami technique has empowered a new paradigm in plasmonics for manipulating light and matter at the nanoscale. This interdisciplinary field has witnessed vigorous growth, outlining a viable route to construct advanced plasmonic architectures with tailored optical properties. However, so far plasmonic systems templated by DNA origami have been restricted to respond to only single stimuli. Despite broad interest and scientific importance, thermal and aptamer-target regulations have not yet been widely utilized to reconfigure three-dimensional plasmonic architectures. In this Letter, we demonstrate a chiral plasmonic nanosystem integrated with split aptamers, which can respond to both thermal and aptamer-target regulations. We show that our dual-responsive system can be noninvasively tuned in a wide range of temperatures, readily correlating thermal control with optical signal changes. Meanwhile, our system can detect specific targets including adenosine triphosphate and cocaine molecules, which further enhance the optical response modulations and in turn influence the thermal tunability.

A DNA-nanoparticle actuator enabling optical monitoring of nanoscale movements induced by an electric field

Merging biological and non-biological matter to fabricate nanoscale assemblies with controllable motion and function is of great interest due to its potential application, for example, in diagnostics and biosensing. Here, we have constructed a DNA-based bionanoactuator that interfaces with biological and non-biological matter via an electric field in a reversibly controllable fashion. The read-out of the actuator is based on motion-induced changes in the plasmon resonance of a gold nanoparticle immobilized to a gold surface by single stranded DNA. The motion of the gold nanoparticle and thus the conformational changes of the DNA under varying electric field were analyzed by dark field spectroscopy. After this basic characterization, another actuator was built utilizing hairpin-DNA coated gold nanoparticles, where the hairpin-DNA induced discrete transitions between two specific open-loop and folded-loop states. These two states and the transition dynamics between them were clearly visible in the actuator behavior. The demonstrated nanoactuator concept could be readily extended to inspection of conformational changes of other biomolecules as well. Besides, this concept enables other possibilities in applications like surface-enhanced Raman spectroscopy and fluorescence enhancement, since the specific wavelength of the plasmon resonance of the actuator can be tuned by the external voltage.

Facing Challenges in Real-Life Application of Surface-Enhanced Raman Scattering: Design and Nanofabrication of Surface-Enhanced Raman Scattering Substrates for Rapid Field Test of Food Contaminants

Surface-enhanced Raman scattering (SERS) is capable of detecting a single molecule with high specificity and has become a promising technique for rapid chemical analysis of agricultural products and foods. With a deeper understanding of the SERS effect and advances in nanofabrication technology, SERS is now on the edge of going out of the laboratory and becoming a sophisticated analytical tool to fulfill various real-world tasks. This review focuses on the challenges that SERS has met in this progress, such as how to obtain a reliable SERS signal, improve the sensitivity and specificity in a complex sample matrix, develop simple and user-friendly practical sensing approach, reduce the running cost, etc. This review highlights the new thoughts on design and nanofabrication of SERS-active substrates for solving these challenges and introduces the recent advances of SERS applications in this area. We hope that our discussion will encourage more researches to address these challenges and eventually help to bring SERS technology out of the laboratory.

DNA Nanotechnology-Enabled Interfacial Engineering for Biosensor Development

Biosensors represent biomimetic analytical tools for addressing increasing needs in medical diagnosis, environmental monitoring, security, and biodefense. Nevertheless, widespread real-world applications of biosensors remain challenging due to limitations of performance, including sensitivity, specificity, speed, and reproducibility. In this review, we present a DNA nanotechnology-enabled interfacial engineering approach for improving the performance of biosensors. We first introduce the main challenges of the biosensing interfaces, especially under the context of controlling the DNA interfacial assembly. We then summarize recent progress in DNA nanotechnology and efforts to harness DNA nanostructures to engineer various biological interfaces, with a particular focus on the use of framework nucleic acids. We also discuss the implementation of biosensors to detect physiologically relevant nucleic acids, proteins, small molecules, ions, and other biomarkers. This review highlights promising applications of DNA nanotechnology in interfacial engineering for biosensors and related areas.

Rhodium nanocubes and nanotripods for highly sensitive ultraviolet surface-enhanced Raman spectroscopy

We report the shape- and wavelength-dependent ultrasensitive label-free detection of adenine on rhodium cube- and tripod-star-like nanoparticles (Rh NPs) using ultraviolet surface-enhanced Raman scattering (UV-SERS). Rh NPs immobilized on a silane-treated glass substrate probed at near-resonant and non-resonant wavelengths served as the SERS platform for the highly reproducible, stable, and real-time detection of adsorbed adenine molecules in the femtomolar region. The sensitivity of SERS-active Rh NPs displaying LSPR in the UV region was exploited for the 266 nm (DUV), 325 nm (UV) and 532 nm (visible) Raman excitation wavelengths. With the 266 nm and 325 nm DUV-UV excitation lines, for the Rh tripod geometry near or pre-resonant excitation being closer to the analyte absorption band combined with the intrinsic UV-LSPR resonant energy produced a SERS enhancement factor as high as 105 and accelerated photoinduced degradations compared to 532 nm for our substrates. Computational results consistent with the experiment clearly demonstrated that the NP SERS enhancement was sensitive to both the intrinsic optical properties of Rh in the UV region and the excitation closer to the LSPR peak producing larger EM enhancements. The wavelength-dependent correlations between the optical properties of the shape-tailored Rh NPs and SERS enhancements envisage the merit and demerit of DUV-UV excitation over visible excitation for Raman measurements. The as-fabricated SERS substrate could also be efficiently recycled using O2 plasma for the detection of other biomolecules. The use of oxide-free transition metal Rh and DUV-UV excitation thereby extends the improved generality of the SERS technique for ultrasensitive bimolecular detection and for gaining a comprehensive understanding of UV-SERS-based applications.

Surface-Enhanced Raman Spectroscopy for Bioanalysis: Reliability and Challenges

Surface-enhanced Raman spectroscopy (SERS) inherits the rich chemical fingerprint information on Raman spectroscopy and gains sensitivity by plasmon-enhanced excitation and scattering. In particular, most Raman peaks have a narrow width suitable for multiplex analysis, and the measurements can be conveniently made under ambient and aqueous conditions. These merits make SERS a very promising technique for studying complex biological systems, and SERS has attracted increasing interest in biorelated analysis. However, there are still great challenges that need to be addressed until it can be widely accepted by the biorelated communities, answer interesting biological questions, and solve fatal clinical problems. SERS applications in bioanalysis involve the complex interactions of plasmonic nanomaterials with biological systems and their environments. The reliability becomes the key issue of bioanalytical SERS in order to extract meaningful information from SERS data. This review provides a comprehensive overview of bioanalytical SERS with the main focus on the reliability issue. We first introduce the mechanism of SERS to guide the design of reliable SERS experiments with high detection sensitivity. We then introduce the current understanding of the interaction of nanomaterials with biological systems, mainly living cells, to guide the design of functionalized SERS nanoparticles for target detection. We further introduce the current status of label-free (direct) and labeled (indirect) SERS detections, for systems from biomolecules, to pathogens, to living cells, and we discuss the potential interferences from experimental design, measurement conditions, and data analysis. In the end, we give an outlook of the key challenges in bioanalytical SERS, including reproducibility, sensitivity, and spatial and time resolution.

DNA-Assembled Advanced Plasmonic Architectures

The interaction between light and matter can be controlled efficiently by structuring materials at a length scale shorter than the wavelength of interest. With the goal to build optical devices that operate at the nanoscale, plasmonics has established itself as a discipline, where near-field effects of electromagnetic waves created in the vicinity of metallic surfaces can give rise to a variety of novel phenomena and fascinating applications. As research on plasmonics has emerged from the optics and solid-state communities, most laboratories employ top-down lithography to implement their nanophotonic designs. In this review, we discuss the recent, successful efforts of employing self-assembled DNA nanostructures as scaffolds for creating advanced plasmonic architectures. DNA self-assembly exploits the base-pairing specificity of nucleic acid sequences and allows for the nanometer-precise organization of organic molecules but also for the arrangement of inorganic particles in space. Bottom-up self-assembly thus bypasses many of the limitations of conventional fabrication methods. As a consequence, powerful tools such as DNA origami have pushed the boundaries of nanophotonics and new ways of thinking about plasmonic designs are on the rise.

DNA metallization: principles, methods, structures, and applications

This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.

Environmentally responsive plasmonic nanoassemblies for biosensing

Assemblies of plasmonic nanoparticles enable new modalities for biosensing.

Sculpting Light by Arranging Optical Components with DNA Nanostructures

DNA nanotechnology has developed into a state where the design and assembly of complex nanoscale structures has become fast, reliable, cost-effective, and accessible to non-experts. Nanometer-precise positioning of organic (dyes, biomolecules, etc.) and inorganic (metal nanoparticles, colloidal quantum dots, etc.) components on DNA nanostructures is straightforward and modular. In this perspective article, we identify the opportunities and challenges that DNA-assembled devices and materials are facing for optical antennas, metamaterials, and sensing applications. With the abilities of arranging hybrid materials in defined geometries, plasmonic effects will, for example, amplify molecular recognition transduction so that single-molecule events will be measureable with simple devices. On the larger scale, DNA nanotechnology has the potential of breaking the symmetry of common self-assembled functional materials creating pre-defined optical properties such as refractive index tuning, Bragg reflection and topological insulation.

Cavity-Type DNA Origami-Based Plasmonic Nanostructures for Raman Enhancement

DNA origami has been established as addressable templates for site-specific anchoring of gold nanoparticles (AuNPs). Given that AuNPs are assembled by charged DNA oligonucleotides, it is important to reduce the charge repulsion between AuNPs-DNA and the template to realize high yields. Herein, we developed a cavity-type DNA origami as templates to organize 30 nm AuNPs, which formed dimer and tetramer plasmonic nanostructures. Transmission electron microscopy images showed that high yields of dimer and tetramer plasmonic nanostructures were obtained by using the cavity-type DNA origami as the template. More importantly, we observed significant Raman signal enhancement from molecules covalently attached to the plasmonic nanostructures, which provides a new way to high-sensitivity Raman sensing.