DNA origami based Au-Ag-core-shell nanoparticle dimers with single-molecule SERS sensitivity

DNA Origami Route for Nanophotonics

The specificity and simplicity of the Watson-Crick base pair interactions make DNA one of the most versatile construction materials for creating nanoscale structures and devices. Among several DNA-based approaches, the DNA origami technique excels in programmable self-assembly of complex, arbitrary shaped structures with dimensions of hundreds of nanometers. Importantly, DNA origami can be used as templates for assembly of functional nanoscale components into three-dimensional structures with high precision and controlled stoichiometry. This is often beyond the reach of other nanofabrication techniques. In this Perspective, we highlight the capability of the DNA origami technique for realization of novel nanophotonic systems. First, we introduce the basic principles of designing and fabrication of DNA origami structures. Subsequently, we review recent advances of the DNA origami applications in nanoplasmonics, single-molecule and super-resolution fluorescent imaging, as well as hybrid photonic systems. We conclude by outlining the future prospects of the DNA origami technique for advanced nanophotonic systems with tailored functionalities.

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.

Hybrid Structure of 2D Layered GaTe with Au Nanoparticles for Ultrasensitive Detection of Aromatic Molecules

Owing to a complex monocline structure and high-density of defects in monocrystalline GaTe, the performance of GaTe-based electronic devices is considerably compromised. Yet, the defects' nature in GaTe could be a merit rather than a shortcoming in other realms. In our work, the density of defects in GaTe films is utilized for a facile decoration of Au nanoparticles (NPs), which allowed us to extend its application potential to the domain of surface enhanced Raman scattering (SERS) for the first time. Two-dimensional (2D) GaTe layered structures are prepared by mechanical exfoliation, and high-density Au NPs are synthesized by immersion of 2D GaTe in HAuCl₄ aqueous solution. By varying the immersion time, the sizes and coverage rate of Au NPs on GaTe can be elaborately tuned. Thanks to the defect nature of GaTe, the maximum coverage amounts to 98%. The hereby achieved Au-NPs-2D-GaTe hybrid structure demonstrates outstanding properties as a superior SERS substrate for ultrasensitive detection of R6G aromatic molecules. Remarkably, the enhancement factor reaches up to 1.6 × 10⁴, and the minimum detectable concentration is 10^-11 M, undercutting that of recently reported Au-NPs-MoS₂ SERS and Au-NPs-graphene SERS substrates which have a similar structure. With superior detection capability and facile preparation, Au-NPs-GaTe SERS substrates can become a perfect choice for the detection of aromatic molecules.

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.

Giant Vesicles with Anchored Tiny Gold Nanowires: Fabrication and Surface-Enhanced Raman Scattering

Sensitivity and reproducibility are two major concerns to improve the performance and extend the range of practical applications of surface-enhanced Raman scattering (SERS). A theoretical report reveals that hot spots formed by gold nanoparticles with a tip-to-tip configuration would generate the maximum electric field enhancement because of the lightning rod effect. In our present study, we constructed a giant vesicle consisting of anchored tiny gold nanowires to provide a high density of sharp tip-to-tip nanogaps for SERS application. The tiny gold nanowires were directly grown and anchored onto the surfaces of polystyrene (PS) microspheres by a seed-mediated method. Then, the removal of PS microspheres by tetrahydrofuran led to the formation of the giant gold vesicles with hierarchical cage structures, providing the sharp tips and high density of hot spots for improving SERS performance. Compared with the nonwire structure (island and inhibited nanoparticle), giant gold vesicles with tiny wires showed a higher SERS enhancement factor (9.90 × 10⁷) and quantitative SERS analysis in the range of 10^-4 to 10^-7 M. In addition, the large-scale giant gold vesicle array on the silica substrate resulted in a high reproducibility of SERS signals with the variation of intensities less than 7.6%.

Biological Molecules-Governed Plasmonic Nanoparticle Dimers with Tailored Optical Behaviors

Self-assembly opens new avenues to direct the organization of nanoparticles (NPs) into discrete structures with predefined configuration and association numbers. Plasmonic NP dimers provide a well-defined system for investigating the plasmonic coupling and electromagnetic (EM) interaction in arrays of NPs. The programmability and structural plasticity of biomolecules offers a convenient platform for constructing of NP dimers in a controllable way. Plasmonic coupling of NPs enables dimers to exhibit tunable optical properties, such as surface-enhanced Raman scattering (SERS), chirality, photoluminescence, and electrochemiluminescence (ECL) properties, which can be tailored by altering the biomolecules, the building blocks with distinct compositions, sizes and morphology, the interparticle distances, as well as the geometric configuration of the constituent NPs. An overview of recent developments in biological molecules-governed NP dimers, the tailored optical behaviors, and challenges in enhancing optical signals and proposing plasmonic biosensors are discussed in this Perspective.

A study on the correlation between the dewetting temperature of Ag film and SERS intensity

The thermally dewetted metal nano-islands have been actively investigated as cost-effective SERS-active substrates with a large area, good reproducibility and repeatability via simple fabrication process. However, the correlation between the dewetting temperature of metal film and SERS intensity hasn't been systematically studied. In this work, taking Ag nano-islands (AgNIs) as an example, we reported a strategy to investigate the correlation between the dewetting temperature of metal film and SERS intensity. We described the morphology evolution of AgNIs on the SiO2 planar substrate in different temperatures and got the quantitative information in surface-limited diffusion process (SLDP) as a function of annealing temperature via classical mean-field nucleation theory. Those functions were further used in the simulation of electromagnetic field to obtain the correlation between the dewetting temperature of Ag film and theoretical analysis. In addition, Raman mapping was done on samples annealed at different temperatures, with R6G as an analyte, to accomplish the analysis of the correlation between the dewetting temperature of Ag film and SERS intensity, which is consistent with the theoretical analysis. For SLDP, we used the morphological characterization of five samples prepared by different annealing temperatures to successfully illustrate the change in SERS intensity with the temperature fluctuation, obtaining a small deviation between the experimental results and theoretic prediction.

High-performance surface-enhanced Raman scattering substrate prepared by self-assembling of silver nanoparticles into the nanogaps of silver nanoislands

We report an effective and simple method to further enhance the surface-enhanced Raman scattering (SERS) by silver (Ag) nanoparticles (AgNPs) self-assembling into the nanogaps of an Ag nanoisland (AgNIs). The AgNIs prepared by dewetting of Ag film created a nanorough surface, which induced the Ag nanoparticles to regularly deposit into the nanogaps. AgNPs and AgNIs samples were also prepared for comparative analysis. Their SERS activities were investigated theoretically and experimentally. Experimental enhancement factors (EFs) for AgNPs, AgNIs, and AgNPs decorated AgNIs substrate (AgNPs-AgNIs) were ∼10⁷, ∼10⁶, ∼10⁸, respectively, with relative standard deviation (RSD) of 66.1%, 12.9%, and 13.2%. Remarkable enhancement (EF≈10⁸) and excellent reproducibility (RSD=13.2%) indicated the AgNPs-AgNIs had a high potential in practical application. Electromagnetic simulation using COMSOL Multiphysics demonstrated that the additional enhancement of the SERS effect could be mainly attributed to the improvement of the local electromagnetic field. Moreover, the deposition process of Ag nanoparticles was analyzed in detail to understand the reproducibility of AgNPs-AgNIs.

Real-time monitoring of plasmon induced dissociative electron transfer to the potential DNA radiosensitizer 8-bromoadenine

The excitation of localized surface plasmons in noble metal nanoparticles (NPs) results in different nanoscale effects such as electric field enhancement, the generation of hot electrons and a temperature increase close to the NP surface. These effects are typically exploited in diverse fields such as surface-enhanced Raman scattering (SERS), NP catalysis and photothermal therapy (PTT). Halogenated nucleobases are applied as radiosensitizers in conventional radiation cancer therapy due to their high reactivity towards secondary electrons. Here, we use SERS to study the transformation of 8-bromoadenine (^8BrA) into adenine on the surface of Au and AgNPs upon irradiation with a low-power continuous wave laser at 532, 633 and 785 nm, respectively. The dissociation of ^8BrA is ascribed to a hot-electron transfer reaction and the underlying kinetics are carefully explored. The reaction proceeds within seconds or even milliseconds. Similar dissociation reactions might also occur with other electrophilic molecules, which must be considered in the interpretation of respective SERS spectra. Furthermore, we suggest that hot-electron transfer induced dissociation of radiosensitizers such as ^8BrA can be applied in the future in PTT to enhance the damage of tumor tissue upon irradiation.

FRET efficiency and antenna effect in multi-color DNA origami-based light harvesting systems

Artificial light harvesting complexes find applications in photosynthesis, photovoltaics and chemical sensors. Here, we present the characterization and optimization of a multi-color artificial light harvesting system on DNA origami structures.

Quantitative Single-Molecule Surface-Enhanced Raman Scattering by Optothermal Tuning of DNA Origami-Assembled Plasmonic Nanoantennas

DNA origami is a powerful approach for assembling plasmonic nanoparticle dimers and Raman dyes with high yields and excellent positioning control. Here we show how optothermal-induced shrinking of a DNA origami template can be employed to control the gap sizes between two 40 nm gold nanoparticles in a range from 1 to 2 nm. The high field confinement achieved with this optothermal approach was demonstrated by detection of surface-enhanced Raman spectroscopy (SERS) signals from single molecules that are precisely placed within the DNA origami template that spans the nanoparticle gap. By comparing the SERS intensity with respect to the field enhancement in the plasmonic hot-spot region, we found good agreement between measurement and theory. Our straightforward approach for the fabrication of addressable plasmonic nanosensors by DNA origami demonstrates a path toward future sensing applications with single-molecule resolution.

Hybrid Structures for Surface-Enhanced Raman Scattering: DNA Origami/Gold Nanoparticle Dimer/Graphene

A combination of three innovative materials within one hybrid structure to explore the synergistic interaction of their individual properties is presented. The unique electronic, mechanical, and thermal properties of graphene are combined with the plasmonic properties of gold nanoparticle (AuNP) dimers, which are assembled using DNA origami nanostructures. This novel hybrid structure is characterized by means of correlated atomic force microscopy and surface-enhanced Raman scattering (SERS). It is demonstrated that strong interactions between graphene and AuNPs result in superior SERS performance of the hybrid structure compared to their individual components. This is particularly evident in efficient fluorescence quenching, reduced background, and a decrease of the photobleaching rate up to one order of magnitude. The versatility of DNA origami structures to serve as interface for complex and precise arrangements of nanoparticles and other functional entities provides the basis to further exploit the potential of the here presented DNA origami-AuNP dimer-graphene hybrid structures.

Structural stability of DNA origami nanostructures in the presence of chaotropic agents

DNA origami represent powerful platforms for single-molecule investigations of biomolecular processes. The required structural integrity of the DNA origami may, however, pose significant limitations regarding their applicability, for instance in protein folding studies that require strongly denaturing conditions. Here, we therefore report a detailed study on the stability of 2D DNA origami triangles in the presence of the strong chaotropic denaturing agents urea and guanidinium chloride (GdmCl) and its dependence on concentration and temperature. At room temperature, the DNA origami triangles are stable up to at least 24 h in both denaturants at concentrations as high as 6 M. At elevated temperatures, however, structural stability is governed by variations in the melting temperature of the individual staple strands. Therefore, the global melting temperature of the DNA origami does not represent an accurate measure of their structural stability. Although GdmCl has a stronger effect on the global melting temperature, its attack results in less structural damage than observed for urea under equivalent conditions. This enhanced structural stability most likely originates from the ionic nature of GdmCl. By rational design of the arrangement and lengths of the individual staple strands used for the folding of a particular shape, however, the structural stability of DNA origami may be enhanced even further to meet individual experimental requirements. Overall, their high stability renders DNA origami promising platforms for biomolecular studies in the presence of chaotropic agents, including single-molecule protein folding or structural switching.

An ion-controlled four-color fluorescent telomeric switch on DNA origami structures

The folding of single-stranded telomeric DNA into guanine (G) quadruplexes is a conformational change that plays a major role in sensing and drug targeting. The telomeric DNA can be placed on DNA origami nanostructures to make the folding process extremely selective for K(+) ions even in the presence of high Na(+) concentrations. Here, we demonstrate that the K(+)-selective G-quadruplex formation is reversible when using a cryptand to remove K(+) from the G-quadruplex. We present a full characterization of the reversible switching between single-stranded telomeric DNA and G-quadruplex structures using Förster resonance energy transfer (FRET) between the dyes fluorescein (FAM) and cyanine3 (Cy3). When attached to the DNA origami platform, the G-quadruplex switch can be incorporated into more complex photonic networks, which is demonstrated for a three-color and a four-color FRET cascade from FAM over Cy3 and Cy5 to IRDye700 with G-quadruplex-Cy3 acting as a switchable transmitter.

One-pot synthesis of gold nanodimers and their use as surface-enhanced Raman scattering tags

Gold dimers consisting of 40 nm-diameter nanospheres show enhancement factors as high as ∼1.8 × 10⁷at the hot-spot level.

Hybridized enhancement of the SERS detection of chemical and bio-marker molecules through Au nanosphere ornamentation of hybrid amorphous/crystalline Si nanoweb nanostructure biochip devices

We report the fabrication of hybrid Si SERS nanobiosensor biochip devices.