Plasmonic DNA-origami nanoantennas for surface-enhanced Raman spectroscopy

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.

Plasmon-Exciton Coupling Using DNA Templates

Coherent energy exchange between plasmons and excitons is a phenomenon that arises in the strong coupling regime resulting in distinct hybrid states. The DNA-origami technique provides an ideal framework to custom-tune plasmon-exciton nanostructures. By employing this well controlled self-assembly process, we realized hybrid states by precisely positioning metallic nanoparticles in a defined spatial arrangement with fixed nanometer-sized interparticle spacing. Varying the nanoparticle diameter between 30 nm and 60 nm while keeping their separation distance constant allowed us to precisely adjust the plasmon resonance of the structure to accurately match the energy frequency of a J-aggregate exciton. With this system we obtained strong plasmon-exciton coupling and studied far-field scattering at the single-structure level. The individual structures displayed normal mode splitting up to 170 meV. The plasmon tunability and the strong field confinement attained with nanodimers on DNA-origami renders an ideal tool to bottom-up assembly plasmon-exciton systems operating at room temperature.

Hot Electron Generation and Cathodoluminescence Nanoscopy of Chiral Split Ring Resonators

Three-dimensional chiral plasmonic nanostructures have been shown to be able to dramatically boost photon-spin selective light-matter interactions, potentially leading to novel photonics, molecular spectroscopy, and light-harvesting applications based on circularly polarized light. Here, we show that chiral split-ring gold nanoresonators interfaced to a wide band gap semiconductor exhibit a contrast in hot-electron transfer rate between left-handed and right-handed visible light that essentially mimics the far-field circular dichroism of the structures. We trace down the origin of this effect to the differential excitation of the thinnest part of the split-ring structures using dichroic-sensitive cathodoluminescence imaging with nanometer spatial resolution. The results highlight the intricate interplay between the near-field and far-field chiral response of a nanostructure and establishes a clear link to the emerging field of hot carrier plasmonics with numerous potential applications in photocatalysis and solar light harvesting.

Highly sensitive and uniform surface-enhanced Raman spectroscopy from grating-integrated plasmonic nanograss

Surface-enhanced Raman scattering (SERS) spectroscopy has found a wide range of applications in biomedicine, food safety and environmental monitoring. However, to date, it is difficult for most SERS substrates to provide an extremely sensitive and highly uniform Raman response simultaneously. Here, we developed a sensitive and uniform SERS sensing strategy based on grating-integrated gold nanograsses (GIGNs), which can amplify the SERS signal up to 10-fold compared to the nanograss without grating (namely on the flat substrate) experimentally. Numerical simulation results show that such an improvement of SERS sensitivity arises from the enhanced hotspots relying on the strong coupling between the localized surface plasmon resonances of individual stripe-regulated gold nanorod assemblies and Wood's anomalies in air and dielectric grating. Importantly, these hotspots on the substrate can be flexibly tailored by adjusting the height and periodicity of the loaded grating. The SERS performances of the GIGNs have further been successfully demonstrated with the label-free detection of adenine and cytosine (DNA bases) molecules at the nanomolar level. Moreover, the GIGNs also presented the uniform spot-to-spot and sample-to-sample SERS signals of the analyte molecules (relative standard deviations down to ∼11% and 13%, respectively). These advantages suggest that our GIGN substrates are of great potential for SERS-related sensing.

Toward Self-Assembled Plasmonic Devices: High-Yield Arrangement of Gold Nanoparticles on DNA Origami Templates

Plasmonic structures allow the manipulation of light with materials that are smaller than the optical wavelength. Such structures can consist of plasmonically active metal nanoparticles and can be fabricated through scalable bottom-up self-assembly on DNA origami templates. To produce functional devices, the precise and high-yield arrangement of each of the nanoparticles on a structure is of vital importance as the absence of a single particle can destroy the functionality of the entire device. Nevertheless, the parameters influencing the yield of the multistep assembly process are still poorly understood. To overcome this deficiency, we employed a test system consisting of a tubular six-helix bundle DNA origami with binding sites for eight oligonucleotide-functionalized gold nanoparticles. We systematically studied the assembly yield as a function of a wide range of parameters such as ionic strength, stoichiometric ratio, oligonucleotide linker chemistry, and assembly kinetics by an automated high-throughput analysis of electron micrographs of the formed heterocomplexes. Our optimized protocols enable particle placement yields up to 98.7% and promise the reliable production of sophisticated DNA-based multiparticle plasmonic devices for applications in photonics, optoelectronics, and nanomedicine.

Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology

Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their myriad applications using examples from the literature. Overall, it is clear that this unique functional combination of nanomaterials has far more to offer than what we have seen to date and as new capabilities for each of these materials are developed, so, too, will new applications emerge.

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

DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 10(10), which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled.

Quantitatively analyzing the mechanism of giant circular dichroism in extrinsic plasmonic chiral nanostructures by tracking the interplay of electric and magnetic dipoles

Plasmonic chirality has drawn much attention because of tunable circular dichroism (CD) and the enhancement for chiral molecule signals. Although various mechanisms have been proposed to explain the plasmonic CD, a quantitative explanation like the ab initio mechanism for chiral molecules, is still unavailable. In this study, a mechanism similar to the mechanisms associated with chiral molecules was analyzed. The giant extrinsic circular dichroism of a plasmonic splitting rectangle ring was quantitatively investigated from a theoretical standpoint. The interplay of the electric and magnetic modes of the meta-structure is proposed to explain the giant CD. We analyzed the interplay using both an analytical coupled electric-magnetic dipole model and a finite element method model. The surface charge distributions showed that the circular current yielded by the splitting rectangle ring causes the ring to behave like a magneton at some resonant modes, which then interact with the electric modes, resulting in a mixing of the two types of modes. The strong interplay of the two mode types is primarily responsible for the giant CD. The analysis of the chiral near-field of the structure shows potential applications for chiral molecule sensing.

Nanostructure-based surface-enhanced Raman scattering biosensors for nucleic acids and proteins

Detection of nucleic acid and protein targets related to human health and safety has attracted widespread attention. Surface-enhanced Raman scattering (SERS) is a powerful tool for biomarker detection because of its ultrahigh detection sensitivity and unique fingerprinting spectra. In this review, we first introduce the development of nanostructure-based SERS-active substrates and SERS nanotags, which greatly influence the performance of SERS biosensors. We then focus on recent advances in SERS biosensors for DNA, microRNA and protein determination, including label-free, labeled and multiplex analyses as well as in vivo imaging. Finally, the prospects and challenges of such nanostructure-based SERS biosensors are discussed.

Increasing the Morphological Stability of DNA-Templated Nanostructures with Surface Hydrophobicity

DNA has been extensively used as a versatile template to assemble inorganic nanoparticles into complex architectures; thanks to its programmability, stability, and long persistence length. But the geometry of self-assembled nanostructures depends on a complex combination of attractive and repulsive forces that can override the shape of a molecular scaffold. In this report, an approach to increase the morphological stability of DNA-templated gold nanoparticle (AuNP) groupings against electrostatic interactions is demonstrated by introducing hydrophobicity on the particle surface. Using single nanostructure spectroscopy, the nanometer-scale distortions of 40 nm diameter AuNP dimers are compared with different hydrophilic, amphiphilic, neutral, and negatively charged surface chemistries, when modifying the local ionic strength. It is observed that, with most ligands, a majority of studied nanostructures deform freely from a stretched geometry to touching particles when increasing the salt concentration while hydrophobicity strongly limits the dimer distortions. Furthermore, an amphiphilic surface chemistry provides DNA-linked AuNP dimers with a high long-term stability against internal aggregation.

Fano resonance assisting plasmonic circular dichroism from nanorice heterodimers for extrinsic chirality

In this work, the circular dichroisms (CD) of nanorice heterodimers consisting of two parallel arranged nanorices with the same size but different materials are investigated theoretically. Symmetry-breaking is introduced by using different materials and oblique incidence to achieve strong CD at the vicinity of Fano resonance peaks. We demonstrate that all Au-Ag heterodimers exhibit multipolar Fano resonances and strong CD effect. A simple quantitative analysis shows that the structure with larger Fano asymmetry factor has stronger CD. The intensity and peak positions of the CD effect can be flexibly tuned in a large range by changing particle size, shape, the inter-particle distance and surroundings. Furthermore, CD spectra exhibit high sensitivity to ambient medium in visible and near infrared regions. Our results here are beneficial for the design and application of high sensitive CD sensors and other related fields.

Fabrication and robotization of ultrasensitive plasmonic nanosensors for molecule detection with Raman scattering

In this work, we introduce the history and mechanisms of surface enhanced Raman scattering (SERS), discuss various techniques for fabrication of state-of-the-art SERS substrates, and review recent work on robotizing plasmonic nanoparticles, especially, the efforts we made on fabrication, characterization, and robotization of Raman nanosensors by design. Our nanosensors, consisting of tri-layer nanocapsule structures, are ultrasensitive, well reproducible, and can be robotized by either electric or magnetic tweezers. Three applications using such SERS nanosensors were demonstrated, including location predictable detection, single-cell bioanalysis, and tunable molecule release and monitoring. The integration of SERS and nanoelectromechanical system (NEMS) devices is innovative in both device concept and fabrication, and could potentially inspire a new device scheme for various bio-relevant applications.

DNA-assembled nanoparticle rings exhibit electric and magnetic resonances at visible frequencies

Metallic nanostructures can be used to manipulate light on the subwavelength scale to create tailored optical material properties. Next to electric responses, artificial optical magnetism is of particular interest but difficult to achieve at visible wavelengths. DNA-self-assembly has proved to serve as a viable method to template plasmonic materials with nanometer precision and to produce large quantities of metallic objects with high yields. We present here the fabrication of self-assembled ring-shaped plasmonic metamolecules that are composed of four to eight single metal nanoparticles with full stoichiometric and geometric control. Scattering spectra of single rings as well as absorption spectra of solutions containing the metamolecules are used to examine the unique plasmonic features, which are compared to computational simulations. We demonstrate that the electric and magnetic plasmon resonance modes strongly correlate with the exact shape of the structures. In particular, our computations reveal the magnetic plasmons only for particle rings of broken symmetries, which is consistent with our experimental data. We stress the feasibility of DNA self-assembly as a method to create bulk plasmonic materials and metamolecules that may be applied as building blocks in plasmonic devices.

Molecular processes studied at a single-molecule level using DNA origami nanostructures and atomic force microscopy

DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.