Plasmonic DNA-origami nanoantennas for surface-enhanced Raman spectroscopy

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 Origami-Engineered Plasmonic Nanoprobes for Targeted Cancer Imaging

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

From Bulk to Single Molecules: Surface-Enhanced Raman Scattering of Cytochrome C Using Plasmonic DNA Origami Nanoantennas

Cytochrome C, an evolutionarily conserved protein, plays pivotal roles in cellular respiration and apoptosis. Understanding its molecular intricacies is essential for both academic inquiry and potential biomedical applications. This study introduces an advanced single-molecule surface-enhanced Raman scattering (SM-SERS) system based on DNA origami nanoantennas (DONAs), optimized to provide unparalleled insights into protein structure and interactions. Our system effectively detects shifts in the Amide III band, thereby elucidating protein dynamics and conformational changes. Additionally, the system permits concurrent observations of oxidation processes and Amide bands, offering an integrated view of protein structural and chemical modifications. Notably, our approach diverges from traditional SM-SERS techniques by de-emphasizing resonance conditions for SERS excitation, aiming to mitigate challenges like peak oversaturation. Our findings underscore the capability of our DONAs to illuminate single-molecule behaviors, even within aggregate systems, providing clarity on molecular interactions and behaviors.

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.

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.

Recent Advances in the 3D Chiral Plasmonic Nanomaterials

From the view of geometry, chirality is that an object cannot overlap with its mirror image, which has been a fundamental scientific problem in biology and chemistry since the 19th century. Chiral inorganic nanomaterials serve as ideal templates for investigating chiral transfer and amplification mechanisms between molecule and bulk materials, garnering widespread attentions. The chiroptical property of chiral plasmonic nanomaterials is enhanced through localized surface plasmon resonance effects, which exhibits distinctive circular dichroism (CD) response across a wide wavelength range. Recently, 3D chiral plasmonic nanomaterials are becoming a focal research point due to their unique characteristics and planar-independence. This review provides an overview of recent progresses in 3D chiral plasmonic nanomaterials studies. It begins by discussing the mechanisms of plasmonic enhancement of molecular CD response, following by a detailed presentation of novel classifications of 3D chiral plasmonic nanomaterials. Finally, the applications of 3D chiral nanomaterials such as biology, sensing, chiral catalysis, photology, and other fields have been discussed and prospected. It is hoped that this review will contribute to the flourishing development of 3D chiral nanomaterials.

Multilayer DNA Origami with Terminal Interfaces That Are Flat and Wide-Area

DNA origami is a popular nanofabrication strategy that employs self-assembly of a long single scaffold strand, typically less than 10 kilobases in length, with hundreds of shorter staple strands into a desired shape. In particular, origami arranged as a single-layer rectangle has proven popular as flat pegboards that can display functionalities at staple-strand breakpoints, off the sides of the constituent double helices, with a ∼5.3 nm rhombic-lattice spacing. For applications that demand tighter spacing, functionalities can be displayed instead on the termini of helices of multilayer DNA origami. However, pegboards with the greatest addressable surface area are often found to be the most versatile. Given the practical limitations of the length of the scaffold that can be easily realized, designs that minimize the length of each helix would have advantages for maximizing the number of helices and therefore the number of addressable pixels on each terminal surface. Here we present an architecture for multilayer DNA origami displaying flush terminal interfaces from over 200 helices that each are only 5.3 turns in length. We characterize an example using cryo-EM imaging paired with single-particle analysis for further analysis of the global structure.

Platinum-DNA Origami Hybrid Structures in Concentrated Hydrogen Peroxide

The DNA origami technique allows fast and large-scale production of DNA nanostructures that stand out with an accurate addressability of their anchor points. This enables the precise organization of guest molecules on the surfaces and results in diverse functionalities. However, the compatibility of DNA origami structures with catalytically active matter, a promising pathway to realize autonomous DNA machines, has so far been tested only in the context of bio-enzymatic activity, but not in chemically harsh reaction conditions. The latter are often required for catalytic processes involving high-energy fuels. Here, we provide proof-of-concept data showing that DNA origami structures are stable in 5 % hydrogen peroxide solutions over the course of at least three days. We report a protocol to couple these to platinum nanoparticles and show catalytic activity of the hybrid structures. We suggest that the presented hybrid structures are suitable to realize catalytic nanomachines combined with precisely engineered DNA nanostructures.

The Effect of Nanoparticle Composition on the Surface-Enhanced Raman Scattering Performance of Plasmonic DNA Origami Nanoantennas

A versatile generation of plasmonic nanoparticle dimers for surface-enhanced Raman scattering (SERS) is presented by combining a DNA origami nanofork and spherical and nonspherical Au or Ag nanoparticles. Combining different nanoparticle species with a DNA origami nanofork to form DNA origami nanoantennas (DONAs), the plasmonic nanoparticle dimers can be optimized for a specific excitation wavelength in SERS. The preparation of such nanoparticle dimers is robust enough to enable the characterization of SERS intensities and SERS enhancement factors of dye-modified DONAs on a single dimer level by measuring in total several thousands of dimers from five different dimer designs, each functionalized with three different Raman reporter molecules and measured at four different excitation wavelengths. Based on these data, SERS enhancement factor (EF) distributions have been determined for each dimer design and excitation wavelengths. The structures and measurement conditions with the highest EFs are suitable for single-molecule SERS (SM-SERS), which is realized by placing single dye molecules into hot spots. We demonstrate that the probability of placing single molecules in a strongly enhancing hot spot for SM-SERS can be increased by using anisotropic nanoparticles with several sharp edges, such as nanoflowers. Combining a Ag nanoparticle with a Au particle in one dimer structure allows for a broadband excitation covering almost the whole visible range. The most versatile plasmonic dimer structure for SERS combines a spherical Ag nanoparticle with a Au nanoflower. Employing the discontinuous Galerkin time domain method, we numerically investigate the bare, symmetric dimers with respect to spectral and near-field properties, showing that, indeed, the nanoflowers induce multiple hot spots located at the edges which surpass the intensity of the spherical dimers, indicating the possibility for SM-SERS. The presented DONA structures and SERS data provide a robust basis for applying such designs as versatile SERS tags and as substrates for SM-SERS measurements.

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.

Amplified Plasmonic Forces from DNA Origami-Scaffolded Single Dyes in Nanogaps

Developing highly enhanced plasmonic nanocavities allows direct observation of light-matter interactions at the nanoscale. With DNA origami, the ability to precisely nanoposition single-quantum emitters in ultranarrow plasmonic gaps enables detailed study of their modified light emission. By developing protocols for creating nanoparticle-on-mirror constructs in which DNA nanostructures act as reliable and customizable spacers for nanoparticle binding, we reveal that the simple picture of Purcell-enhanced molecular dye emission is misleading. Instead, we show that the enhanced dipolar dye polarizability greatly amplifies optical forces acting on the facet Au atoms, leading to their rapid destabilization. Using different dyes, we find that emission spectra are dominated by inelastic (Raman) scattering from molecules and metals, instead of fluorescence, with molecular bleaching also not evident despite the large structural rearrangements. This implies that the competition between recombination pathways demands a rethink of routes to quantum optics using plasmonics.

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.

Lab-on-a-DNA origami: nanoengineered single-molecule platforms

DNA origami nanostructures are self-assembled into almost arbitrary two- and three-dimensional shapes from a long, single-stranded viral scaffold strand and a set of short artificial oligonucleotides. Each DNA strand can be functionalized individually using well-established DNA chemistry, representing addressable sites that allow for the nanometre precise placement of various chemical entities such as proteins, molecular chromophores, nanoparticles, or simply DNA motifs. By means of microscopic and spectroscopic techniques, these entities can be visualized or detected, and either their mutual interaction or their interaction with external stimuli such as radiation can be studied. This gives rise to the Lab-on-a-DNA origami approach, which is introduced in this Feature Article, and the state-of-the-art is summarized with a focus on light-harvesting nanoantennas and DNA platforms for single-molecule analysis either by optical spectroscopy or atomic force microscopy (AFM). Light-harvesting antennas can be generated by the precise arrangement of chromophores to channel and direct excitation energy. At the same time, plasmonic nanoparticles represent a complementary approach to focus light on the nanoscale. Plasmonic nanoantennas also allow for the observation of single molecules either by Raman scattering or fluorescence spectroscopy and DNA origami platforms provide unique opportunities to arrange nanoparticles and molecules to be studied. Finally, the analysis of single DNA motifs by AFM allows for an investigation of radiation-induced processes in DNA with unprecedented detail and accuracy.

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.

A switchable DNA origami/plasmonic hybrid device with a precisely tuneable DNA-free interparticle gap

We here show a reconfigurable DNA/plasmonic nanodevice with a precisely tunable and DNA-free interparticle gap. The nanodevice comprises two DNA boxes for the size-selective incorporation of nanoparticles in a face-to-face orientation and an underlying switchable DNA platform for the controlled and reversible adjustment of the interparticle distance.

Near-unity Raman β-factor of surface-enhanced Raman scattering in a waveguide

The Raman scattering of light by molecular vibrations is a powerful technique to fingerprint molecules through their internal bonds and symmetries. Since Raman scattering is weak¹, methods to enhance, direct and harness it are highly desirable, and this has been achieved using optical cavities², waveguides^3-6 and surface-enhanced Raman scattering (SERS)^7-9. Although SERS offers dramatic enhancements^2,6,10,11 by localizing light within vanishingly small hot-spots in metallic nanostructures, these tiny interaction volumes are only sensitive to a few molecules, yielding weak signals¹². Here we show that SERS from 4-aminothiophenol molecules bonded to a plasmonic gap waveguide is directed into a single mode with >99% efficiency. Although sacrificing a confinement dimension, we find a SERS enhancement of ~10³ times across a broad spectral range enabled by the waveguide's larger sensing volume and non-resonant waveguide mode. Remarkably, this waveguide SERS is bright enough to image Raman transport across the waveguides, highlighting the role of nanofocusing^13-15 and the Purcell effect¹⁶. By analogy to the β-factor from laser physics^10,17-20, the near-unity Raman β-factor we observe exposes the SERS technique to alternative routes for controlling Raman scattering. The ability of waveguide SERS to direct Raman scattering is relevant to Raman sensors based on integrated photonics^7-9 with applications in gas sensing and biosensing.

Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering

The study of biologically relevant molecules and their interaction with external stimuli on a single molecular scale is of high importance due to the availability of distributed rather than averaged information. Surface enhanced Raman scattering (SERS) provides direct chemical information, but is rather challenging on the single molecule (SM) level, where it is often assumed to require a direct contact of analyte molecules with the metal surface. Here, we detect and investigate the molecular states of single hemin by SM-SERS. A DNA aptamer based G-quadruplex mediated recognition of hemin directs its placement in the SERS hot-spot of a DNA Origami Nanofork Antenna (DONA). The configuration of the DONA structure allows the molecule to be trapped at the plasmonic hot-spot preferentially in no-contact configuration with the metal surface. Owing to high field enhancement at the plasmonic hot spot, the detection of a single folded G-quadruplex becomes possible. For the first time, we present a systematic study by SM-SERS where most hemin molecule adopt a high spin and oxidation state (III) that showed state crossover to low spin upon strong-field-ligand binding. The present study therefore, provides a platform for studying biologically relevant molecules and their properties at SM sensitivity along with demonstrating a conceptual advancement towards successful monitoring of single molecular chemical interaction using DNA aptamers.

DNA-mediated dynamic plasmonic nanostructures: assembly, actuation, optical properties, and biological applications

Recent advances in DNA technology have made it possible to combine with the plasmonics to fabricate reconfigurable dynamic nanodevices with extraordinary property and function. These DNA-mediated plasmonic nanostructures have been investigated for a variety of unique and beneficial physicochemical properties and their dynamic behavior has been controlled by endogenous or exogenous stimuli for a variety of interesting biological applications. In this perspective, the recent efforts to use the DNA nanostructures as molecular linkers for fabricating dynamic plasmonic nanostructures are reviewed. Next, the actuation media for triggering the dynamic behavior of plasmonic nanostructures and the dynamic response in optical features are summarized. Finally, the applications, remaining challenges and perspectives of the DNA-mediated dynamic plasmonic nanostructures are discussed.

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.

Freeze-Driven Adsorption of Poly-A DNA on Gold Nanoparticles: From a Stable Biointerface to Plasmonic Dimers

Increasing attention is paid to poly-adenine (poly-A) DNA-functionalized gold nanoparticles due to the high cost of thiols. Freezing is an effective approach for immobilizing poly-A DNA on gold nanoparticles, but its mechanism remains elusive. To cope with this issue, in this paper, some experimental insights are provided. It is shown that (1) the DNA loading density is independent of the length of poly-A. (2) DNA is densely packed on gold nanoparticles, and the biointerface is peculiarly stable, which is not in line with the existing "wrapping" model. (3) Using a DNA-staining dye, thiazole orange, it is shown that poly-A duplex structures are formed on the surface of gold nanoparticles, with evidence given by fluorescence and Raman measurements. An alternative model involving stable poly-A duplexes anchored by finite terminal adenines is proposed. Based on it, a strategy for constructing plasmonic dimers is developed, using freeze-driven adsorption of a DNA sequence with poly-adenine at both ends. This work provides insights into the reaction between poly-A DNA and AuNPs upon freezing and is expected to facilitate related research in biosensor development and nanotechnology.

Resonance mode analysis of DNA self-assembled metamolecules with an effective refractive index model

We investigated the feasibility of a simple effective refractive index model based on the finite-difference time-domain method for DNA self-assembled metamolecules. Metamolecules were fabricated with Au nanoparticles (AuNPs) and a two-layer rectangular DNA template. Simulated scattering spectra for AuNPs placed on the template (n_eff= 1.3), self-assembled DNA dimers (n_eff= 1.34), and quadrumers (n_eff= 1.5) matched well with experimental results. Dipolar and Fano-like resonances were predicted from the calculated field distribution. These results indicate that we can easily estimate the resonance mode of fabricated metamolecules on a glass substrate, even when they are surrounded by complex materials such as DNA, by using a simple refractive index model.

Development of Synthetic DNA Circuit and Networks for Molecular Information Processing

Deoxyribonucleic acid (DNA), a genetic material, encodes all living information and living characteristics, e.g., in cell, DNA signaling circuits control the transcription activities of specific genes. In recent years, various DNA circuits have been developed to implement a wide range of signaling and for regulating gene network functions. In particular, a synthetic DNA circuit, with a programmable design and easy construction, has become a crucial method through which to simulate and regulate DNA signaling networks. Importantly, the construction of a hierarchical DNA circuit provides a useful tool for regulating gene networks and for processing molecular information. Moreover, via their robust and modular properties, DNA circuits can amplify weak signals and establish programmable cascade systems, which are particularly suitable for the applications of biosensing and detecting. Furthermore, a biological enzyme can also be used to provide diverse circuit regulation elements. Currently, studies regarding the mechanisms and applications of synthetic DNA circuit are important for the establishment of more advanced artificial gene regulation systems and intelligent molecular sensing tools. We therefore summarize recent relevant research progress, contributing to the development of nanotechnology-based synthetic DNA circuits. By summarizing the current highlights and the development of synthetic DNA circuits, this paper provides additional insights for future DNA circuit development and provides a foundation for the construction of more advanced DNA circuits.

Synthesis, Assembly, Optical Properties, and Sensing Applications of Plasmonic Gap Nanostructures

Plasmonic gap nanostructures (PGNs) have been extensively investigated mainly because of their strongly enhanced optical responses, which stem from the high intensity of the localized field in the nanogap. The recently developed methods for the preparation of versatile nanogap structures open new avenues for the exploration of unprecedented optical properties and development of sensing applications relying on the amplification of various optical signals. However, the reproducible and controlled preparation of highly uniform plasmonic nanogaps and the prediction, understanding, and control of their optical properties, especially for nanogaps in the nanometer or sub-nanometer range, remain challenging. This is because subtle changes in the nanogap significantly affect the plasmonic response and are of paramount importance to the desired optical performance and further applications. Here, recent advances in the synthesis, assembly, and fabrication strategies, prediction and control of optical properties, and sensing applications of PGNs are discussed, and perspectives toward addressing these challenging issues and the future research directions are presented.

Bench-Top Fabrication of Single-Molecule Nanoarrays by DNA Origami Placement

Large-scale nanoarrays of single biomolecules enable high-throughput assays while unmasking the underlying heterogeneity within ensemble populations. Until recently, creating such grids which combine the advantages of microarrays and single-molecule experiments (SMEs) has been particularly challenging due to the mismatch between the size of these molecules and the resolution of top-down fabrication techniques. DNA origami placement (DOP) combines two powerful techniques to address this issue: (i) DNA origami, which provides a ∼100 nm self-assembled template for single-molecule organization with 5 nm resolution and (ii) top-down lithography, which patterns these DNA nanostructures, transforming them into functional nanodevices via large-scale integration with arbitrary substrates. Presently, this technique relies on state-of-the-art infrastructure and highly trained personnel, making it prohibitively expensive for researchers. Here, we introduce a cleanroom-free, $1 benchtop technique to create meso-to-macro-scale DNA origami nanoarrays using self-assembled colloidal nanoparticles, thereby circumventing the need for top-down fabrication. We report a maximum yield of 74%, 2-fold higher than the statistical limit of 37% imposed on non-specific molecular loading alternatives. Furthermore, we provide a proof-of-principle for the ability of this nanoarray platform to transform traditionally low-throughput, stochastic, single-molecule assays into high-throughput, deterministic ones, without compromising data quality. Our approach has the potential to democratize single-molecule nanoarrays and demonstrates their utility as a tool for biophysical assays and diagnostics.

DNA-based plasmonic nanostructures and their optical and biomedical applications

In the past few decades, DNA nanotechnology has been developed a lot due to their appealing features such as structural programmability and easy functionalization. In the emerging field of DNA nanotechnology, DNA molecules are regarded not only as biological information carriers but also as building blocks in the assembly of various two-dimensional and three-dimensional nanostructures, serving as outstanding templates for the bottom-up fabrication of plasmonic nanostructures. By arranging nanoparticles with different components and morphologies on the predesigned DNA templates, various static and dynamic plasmonic nanostructures with tailored optical properties have been obtained. In this review, we summarized recent advances in the design and construction of static and dynamic DNA-based plasmonic nanostructures. In addition, we addressed their emerging applications in the fields of optics and biosensors. At the end of this review, the open questions and future directions of DNA-based plasmonic nanostructure are also discussed.

Cryo-Electron Microscopy and Mass Analysis of Oligolysine-Coated DNA Nanostructures

Cationic coatings can enhance the stability of synthetic DNA objects in low ionic strength environments such as physiological fluids. Here, we used single-particle cryo-electron microscopy (cryo-EM), pseudoatomic model fitting, and single-molecule mass photometry to study oligolysine and polyethylene glycol (PEG)-oligolysine-coated multilayer DNA origami objects. The coatings preserve coarse structural features well on a resolution of multiple nanometers but can also induce deformations such as twisting and bending. Higher-density coatings also led to internal structural deformations in the DNA origami test objects, in which a designed honeycomb-type helical lattice was deformed into a more square-lattice-like pattern. Under physiological ionic strength, where the uncoated objects disassembled, the coated objects remained intact but they shrunk in the helical direction and expanded in the direction perpendicular to the helical axis. Helical details like major/minor grooves and crossover locations were not discernible in cryo-EM maps that we determined of DNA origami coated with oligolysine and PEG-oligolysine, whereas these features were visible in cryo-EM maps determined from the uncoated reference objects. Blunt-ended double-helical interfaces remained accessible underneath the coating and may be used for the formation of multimeric DNA origami assemblies that rely on stacking interactions between blunt-ended helices. The ionic strength requirements for forming multimers from coated DNA origami differed from those needed for uncoated objects. Using single-molecule mass photometry, we found that the mass of coated DNA origami objects prior to and after incubation in low ionic strength physiological conditions remained unchanged. This finding indicated that the coating effectively prevented strand dissociation but also that the coating itself remained stable in place. Our results validate oligolysine coatings as a powerful stabilization method for DNA origami but also reveal several potential points of failure that experimenters should watch to avoid working with false premises.

Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold

SYBR Gold is a commonly used and particularly bright fluorescent DNA stain, however, its chemical structure is unknown and its binding mode to DNA remains controversial. Here, we solve the structure of SYBR Gold by NMR and mass spectrometry to be [2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium] and determine its extinction coefficient. We quantitate SYBR Gold binding to DNA using two complementary approaches. First, we use single-molecule magnetic tweezers (MT) to determine the effects of SYBR Gold binding on DNA length and twist. The MT assay reveals systematic lengthening and unwinding of DNA by 19.1° ± 0.7° per molecule upon binding, consistent with intercalation, similar to the related dye SYBR Green I. We complement the MT data with spectroscopic characterization of SYBR Gold. The data are well described by a global binding model for dye concentrations ≤2.5 μM, with parameters that quantitatively agree with the MT results. The fluorescence increases linearly with the number of intercalated SYBR Gold molecules up to dye concentrations of ∼2.5 μM, where quenching and inner filter effects become relevant. In summary, we provide a mechanistic understanding of DNA-SYBR Gold interactions and present practical guidelines for optimal DNA detection and quantitative DNA sensing applications using SYBR Gold.

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.

Site-specific facet protection of gold nanoparticles inside a 3D DNA origami box: a tool for molecular plasmonics

Bare gold nanocubes and nanospheres with different sizes are incorporated into a rationally designed 3D DNA origami box. The encaged particles expose a gold surface accessible for subsequent site-specific functionalization, for example, for applications in molecular plasmonics such as SERS or SEF.

Single plasmonic nanostructures for biomedical diagnosis

The field of single nanoparticle plasmonics has grown enormously. There is no doubt that a wide diversity of the nanoplasmonic techniques and nanostructures represents a tremendous opportunity for fundamental biomedical studies as well as sensing and imaging applications. Single nanoparticle plasmonic biosensors are efficient in label-free single-molecule detection, as well as in monitoring real-time binding events of even several biomolecules. In the present review, we have discussed the prominent advantages and advances in single particle characterization and synthesis as well as new insight into and information on biomedical diagnosis uniquely obtained using single particle approaches. The approaches include the fundamental studies of nanoplasmonic behavior, two typical methods based on refractive index change and characteristic light intensity change, exciting innovations of synthetic strategies for new plasmonic nanostructures, and practical applications using single particle sensing, imaging, and tracking. The basic sphere and rod nanostructures are the focus of extensive investigations in biomedicine, while they can be programmed into algorithmic assemblies for novel plasmonic diagnosis. Design of single nanoparticles for the detection of single biomolecules will have far-reaching consequences in biomedical diagnosis.

DNA Origami-Enabled Plasmonic Sensing

The reliable programmability of DNA origami makes it an extremely attractive tool for bottom-up self-assembly of complex nanostructures. Utilizing this property for the tuned arrangement of plasmonic nanoparticles holds great promise particularly in the field of biosensing. Plasmonic particles are beneficial for sensing in multiple ways, from enhancing fluorescence to enabling a visualization of the nanoscale dynamic actuation via chiral rearrangements. In this Perspective, we discuss the recent developments and possible future directions of DNA origami-enabled plasmonic sensing systems. We start by discussing recent advancements in the area of fluorescence-based plasmonic sensing using DNA origami. We then move on to surface-enhanced Raman spectroscopy sensors followed by chiral sensing, both utilizing DNA origami nanostructures. We conclude by providing our own views on the future prospects for plasmonic biosensors enabled using DNA origami.

Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures

We present a technique to determine the orientation of single fluorophores attached to DNA origami structures based on two measurements. First, the orientation of the absorption transition dipole of the molecule is determined through a polarization-resolved excitation measurement. Second, the orientation of the DNA origami structure is obtained from a DNA-PAINT nanoscopy measurement. Both measurements are performed consecutively on a fluorescence wide-field microscope. We employed this approach to study the orientation of single ATTO 647N, ATTO 643, and Cy5 fluorophores covalently attached to a 2D rectangular DNA origami structure with different nanoenvironments, achieved by changing both the fluorophores' binding position and immediate vicinity. Our results show that when fluorophores are incorporated with additional space, for example, by omitting nucleotides in an elsewise double-stranded environment, they tend to stick to the DNA and to adopt a preferred orientation that depends more on the specific molecular environment than on the fluorophore type. With the aid of all-atom molecular dynamics simulations, we rationalized our observations and provide insight into the fluorophores' probable binding modes. We believe this work constitutes an important step toward manipulating the orientation of single fluorophores in DNA origami structures, which is vital for the development of more efficient and reproducible self-assembled nanophotonic devices.

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.

DNA Origami-Enabled Biosensors

Biosensors are small but smart devices responding to the external stimulus, widely used in many fields including clinical diagnosis, healthcare and environment monitoring, etc. Moreover, there is still a pressing need to fabricate sensitive, stable, reliable sensors at present. DNA origami technology is able to not only construct arbitrary shapes in two/three dimension but also control the arrangement of molecules with different functionalities precisely. The functionalization of DNA origami nanostructure endows the sensing system potential of filling in weak spots in traditional DNA-based biosensor. Herein, we mainly review the construction and sensing mechanisms of sensing platforms based on DNA origami nanostructure according to different signal output strategies. It will offer guidance for the application of DNA origami structures functionalized by other materials. We also point out some promising directions for improving performance of biosensors.

MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems

Although the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of experimental characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resolution simulation framework, mrdna, that, in 30 min or less, can produce an atomistic-resolution structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equilibrium structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e. wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied electric field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and molecular graphics tools.

Plasmonic Enhancement of Two-Photon Excitation Fluorescence by Colloidal Assemblies of Very Small AuNPs Templated on M13 Phage

In this study, an engineered M13 bacteriophage was examined as a biological template to create a well-defined spacing between very small gold nanoparticles (AuNPs 3-13 nm). The effect of the AuNP particle size on the enhancement of the nonlinear process of two-photon excitation fluorescence (2PEF) was investigated. Compared to conventional (one-photon) microscopy techniques, such nonlinear processes are less susceptible to scattering given that the density of background-scattered photons is too low to generate a detectable signal. Besides this, the use of very small AuNPs in 2PEF microscopy becomes more advantageous because individual "isolated" AuNPs of this size do not sufficiently enhance 2PEF to produce a detectable signal, resulting in even less background signal. To investigate the 2PEF of the AuNP-M13 assemblies, a variety of sample preparation approaches are tested, and surface-enhanced Raman spectroscopy (SERS) is employed to study the strength of plasmon coupling within the gaps of AuNPs assembled on the M13 template. Results indicate that assemblies prepared with 9-13 nm AuNP were able to clearly label Escherichia coli cells and produce a 2PEF signal that was orders of magnitude higher than the isolated AuNP (below the threshold of detection). This study thus provides a better understanding of the opportunities and limitations relevant to the use of such small AuNPs within colloidal plasmonic assemblies, for applications in biodetection or as imaging contrast agents.

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.

Gold Nanorod Assemblies: The Roles of Hot-Spot Positioning and Anisotropy in Plasmon Coupling and SERS

Plasmon-coupled colloidal nanoassemblies with carefully sculpted "hot-spots" and intense surface-enhanced Raman scattering (SERS) are in high demand as photostable and sensitive plasmonic nano-, bio-, and chemosensors. When maximizing SERS signals, it is particularly challenging to control the hot-spot density, precisely position the hot-spots to intensify the plasmon coupling, and introduce the SERS molecule in those intense hot-spots. Here, we investigated the importance of these factors in nanoassemblies made of a gold nanorod (AuNR) core and spherical nanoparticle (AuNP) satellites with ssDNA oligomer linkers. Hot-spot positioning at the NR tips was made possible by selectively burying the ssDNA in the lateral facets via controlled Ag overgrowth while retaining their hybridization and assembly potential at the tips. This strategy, with slight alterations, allowed us to form nanoassemblies that only contained satellites at the NR tips, i.e., directional anisotropic nanoassemblies; or satellites randomly positioned around the NR, i.e., nondirectional nanoassemblies. Directional nanoassemblies featured strong plasmon coupling as compared to nondirectional ones, as a result of strategically placing the hot-spots at the most intense electric field position of the AuNR, i.e., retaining the inherent plasmon anisotropy. Furthermore, as the dsDNA was located in these anisotropic hot-spots, this allowed for the tag-free detection down to 10 dsDNA and a dramatic SERS enhancement of 1.6 × 108 for the SERS tag SYBR gold, which specifically intercalates into the dsDNA. This dramatic SERS performance was made possible by manipulating the anisotropy of the nanoassemblies, which allowed us to emphasize the critical role of hot-spot positioning and SERS molecule positioning in nanoassemblies.

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.

Plasmonic Nanoassemblies: Tentacles Beat Satellites for Boosting Broadband NIR Plasmon Coupling Providing a Novel Candidate for SERS and Photothermal Therapy

Optical theranostic applications demand near-infrared (NIR) localized surface plasmon resonance (LSPR) and maximized electric field at nanosurfaces and nanojunctions, aiding diagnosis via Raman or optoacoustic imaging, and photothermal-based therapies. To this end, multiple permutations and combinations of plasmonic nanostructures and molecular "glues" or linkers are employed to obtain nanoassemblies, such as nanobranches and core-satellite morphologies. An advanced nanoassembly morphology comprising multiple linear tentacles anchored onto a spherical core is reported here. Importantly, this core-multi-tentacle-nanoassembly (CMT) benefits from numerous plasmonic interactions between multiple 5 nm gold nanoparticles (NPs) forming each tentacle as well as tentacle to core (15 nm) coupling. This results in an intense LSPR across the "biological optical window" of 650-1100 nm. It is shown that the combined interactions are responsible for the broadband LSPR and the intense electric field, otherwise not achievable with core-satellite morphologies. Further the sub 80 nm CMTs boosted NIR-surface-enhanced Raman scattering (SERS), with detection of SERS labels at 47 × 10^-9 m, as well as lower toxicity to noncancerous cell lines (human fibroblast Wi38) than observed for cancerous cell lines (human breast cancer MCF7), presents itself as an attractive candidate for use as biomedical theranostics agents.

Oliveira O, Mejía-Salazar JR. Chiral Plasmonics and Their Potential for Point-of-Care Biosensing Applications

There has been growing interest in using strong field enhancement and light localization in plasmonic nanostructures to control the polarization properties of light. Various experimental techniques are now used to fabricate twisted metallic nanoparticles and metasurfaces, where strongly enhanced chiral near-fields are used to intensify circular dichroism (CD) signals. In this review, state-of-the-art strategies to develop such chiral plasmonic nanoparticles and metasurfaces are summarized, with emphasis on the most recent trends for the design and development of functionalizable surfaces. The major objective is to perform enantiomer selection which is relevant in pharmaceutical applications and for biosensing. Enhanced sensing capabilities are key for the design and manufacture of lab-on-a-chip devices, commonly named point-of-care biosensing devices, which are promising for next-generation healthcare systems.

Tagged Core-Satellite Nanoassemblies: Role of Assembling Sequence on Surface-Enhanced Raman Scattering (SERS) Performance

Plasmonic nanoassemblies with amplified optical responses are attractive as chemo/bio sensors and diagnostic tracking agents. For real-life implementation, such nanostructures require a well-designed and controlled formation for maximizing the optical amplification. Forming these nanoassemblies typically requires numerous steps; however, the importance of the sequence of the steps is typically not discussed. Thus, here we have investigated the role of the sequence of tagging (or labeling, barcoding) of such plasmonic nanoassemblies with Raman active molecules in a quest to maximize the surface-enhanced Raman scattering (SERS) enhancement that could be achieved from the nanoassemblies. We have chosen the core-satellite nanoassembly arrangement to study the role of tagging sequence because it allows us to keep structural parameters constant that would otherwise influence the SERS amplification. We demonstrate that incorporating the tag molecule at an assembly point before formation of the nanojunctions leads to more tag molecules being positioned at the core-satellite nanojunctions, thereby resulting in higher SERS signal enhancement. This will thus prove to be a useful tool in fully utilizing the nanoassembly morphology generated hot-spot and maximizing its SERS performance.

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.

Surface-Enhanced Raman Spectroscopy Based on a Silver-Film Semi-Coated Nanosphere Array

In this paper, we present a convenient and economical method to fabricate a silver (Ag)-film semi-coated polystyrene (PS) nanosphere array substrate for surface-enhanced Raman spectroscopy (SERS). The SERS substrate was fabricated using the modified self-assembled method combined with the vacuum thermal evaporation method. By changing the thickness of the Ag film, the surface morphology of the Ag film coated on the PS nanospheres can be adjusted to obtain the optimized localized surface plasmonic resonance (LSPR) effect. The 3D-finite-difference time-domain simulation results show that the SERS substrate with an Ag film thickness of 10 nm has tens of times the electric field intensity enhancement. The Raman examination results show that the SERS substrate has excellent reliability and sensitivity using rhodamine-6G (R6G) and rhodamine-B (RB) as target analytes, and the Raman sensitivity can reach 10⁻¹⁰ M. Meanwhile, the SERS substrate has excellent uniformity based on the Raman mapping result. The Raman enhancement factor of the SERS substrate was estimated to be 5.1 × 10⁶. This kind of fabrication method for the SERS substrate may be used in some applications of Raman examination.

Directing Single-Molecule Emission with DNA Origami-Assembled Optical Antennas

We demonstrate the capability of DNA self-assembled optical antennas to direct the emission of an individual fluorophore, which is free to rotate. DNA origami is used to fabricate optical antennas composed of two colloidal gold nanoparticles separated by a predefined gap and to place a single Cy5 fluorophore near the gap center. Although the fluorophore is able to rotate, its excitation and far-field emission is mediated by the antenna, with the emission directionality following a dipolar pattern according to the antenna main resonant mode. This work is intended to set out the basis for manipulating the emission pattern of single molecules with self-assembled optical antennas based on colloidal nanoparticles.

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.