Shifting molecular localization by plasmonic coupling in a single-molecule mirage

Thermometries for Single Nanoparticles Heated with Light

The development of efficient nanoscale photon absorbers, such as plasmonic or high-index dielectric nanostructures, allows the remotely controlled release of heat on the nanoscale using light. These photothermal nanomaterials have found applications in various research and technological fields, ranging from materials science to biology. However, measuring the nanoscale thermal fields remains an open challenge, hindering full comprehension and control of nanoscale photothermal phenomena. Here, we review and discuss existent thermometries suitable for single nanoparticles heated under illumination. These methods are classified in four categories according to the region where they assess temperature: (1) the average temperature within a diffraction-limited volume, (2) the average temperature at the immediate vicinity of the nanoparticle surface, (3) the temperature of the nanoparticle itself, and (4) a map of the temperature around the nanoparticle with nanoscale spatial resolution. In the latter, because it is the most challenging and informative type of method, we also envisage new combinations of technologies that could be helpful in retrieving nanoscale temperature maps. Finally, we analyze and provide examples of strategies to validate the results obtained using different thermometry methods.

Spatial Distributions of Single-Molecule Reactivity in Plasmonic Catalysis

Plasmonic catalysts have the potential to accelerate and control chemical reactions with light by exploiting localized surface plasmon resonances. However, the mechanisms governing plasmonic catalysis are not simple to decouple. Several plasmon-derived phenomena, such as electromagnetic field enhancements, temperature, or the generation of charge carriers, can affect the reactivity of the system. These effects are convoluted with the inherent (nonplasmonic) catalytic properties of the metal surface. Disentangling these coexisting effects is challenging but is the key to rationally controlling reaction pathways and enhancing reaction rates. This study utilizes super-resolution fluorescence microscopy to examine the mechanisms of plasmonic catalysis at the single-particle level. The reduction reaction of resazurin to resorufin in the presence of Au nanorods coated with a porous silica shell is investigated in situ. This allows the determination of reaction rates with a single-molecule sensitivity and subparticle resolution. By variation of the irradiation wavelength, it is possible to examine two different regimes: photoexcitation of the reactant molecules and photoexcitation of the nanoparticle's plasmon resonance. In addition, the measured spatial distribution of reactivity allows differentiation between superficial and far-field effects. Our results indicate that the reduction of resazurin can occur through more than one reaction pathway, being most efficient when the reactant is photoexcited and is in contact with the Au surface. In addition, it was found that the spatial distribution of enhancements varies, depending on the underlying mechanism. These findings contribute to the fundamental understanding of plasmonic catalysis and the rational design of future plasmonic nanocatalysts.

Single-emitter super-resolved imaging of radiative decay rate enhancement in dielectric gap nanoantennas

High refractive index dielectric nanoantennas strongly modify the decay rate via the Purcell effect through the design of radiative channels. Due to their dielectric nature, the field is mainly confined inside the nanostructure and in the gap, which is hard to probe with scanning probe techniques. Here we use single-molecule fluorescence lifetime imaging microscopy (smFLIM) to map the decay rate enhancement in dielectric GaP nanoantenna dimers with a median localization precision of 14 nm. We measure, in the gap of the nanoantenna, decay rates that are almost 30 times larger than on a glass substrate. By comparing experimental results with numerical simulations we show that this large enhancement is essentially radiative, contrary to the case of plasmonic nanoantennas, and therefore has great potential for applications such as quantum optics and biosensing.

Unidirectional Meta-Emitters Based on the Kerker Condition Assembled by DNA Origami

Optical quantum emitters near nanostructures have access to additional relaxation channels and thus exhibit structure-dependent emission properties, including quantum yield and emission directionality. A well-engineered quantum emitter-plasmonic nanostructure hybrid can be considered as an optical meta-emitter consisting of a transmitting nanoantenna driven by an optical-frequency generator. In this work, the DNA origami fabrication method is used to construct ultracompact unidirectional meta-emitters composed of a plasmonic trimer nanoantenna driven by a single dye molecule. The origami is designed to bring the dye to the gap to simultaneously excite the electric and magnetic dipole modes of the trimer nanoantenna. The interference of these modes fulfills the Kerker condition at the fluorophore's emission band, enabling unidirectional emission. We report unidirectional emission from a single molecule with a front-to-back ratio of up to 10.7 dB accompanied by a maximum emission enhancement of 23-fold.

Defocused imaging-based quantification of plasmon-induced distortion of single emitter emission

Optical properties of single emitters can be significantly improved through the interaction with plasmonic structures, leading to enhanced sensing and imaging capabilities. In turn, single emitters can act as sensitive probes of the local electromagnetic field surrounding plasmonic structures, furnishing fundamental insights into their physics and guiding the design of novel plasmonic devices. However, the interaction of emitters in the proximity to a plasmonic nanostructure causes distortion, which hinders precise estimation of position and polarization state and is one of the reasons why detection and quantification of molecular processes yet remain fundamentally challenging in this era of super-resolution. Here, we investigate axially defocused images of a single fluorescent emitter near metallic nanostructure, which encode emitter positions and can be acquired in the far-field with high sensitivity, while analyzing the images with pattern matching algorithm to explore emitter-localized surface plasmon interaction and retrieve information regarding emitter positions. Significant distortion in defocused images of fluorescent beads and quantum dots near nanostructure was observed and analyzed by pattern matching and finite-difference time-domain methods, which revealed that the distortion arises from the emitter interaction with nanostructure. Pattern matching algorithm was also adopted to estimate the lateral positions of a dipole that models an emitter utilizing the distorted defocused images and achieved improvement by more than 3 times over conventional diffraction-limited localization methods. The improvement by defocused imaging is expected to provide a way of enhancing reliability when using plasmonic nanostructure and diversifying strategies for various imaging and sensing modalities.

Recent Advances in DNA Origami-Engineered Nanomaterials and Applications

DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.

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

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

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.

Super-resolution Imaging of Plasmonic Near-Fields: Overcoming Emitter Mislocalizations

Plasmonic nano-objects have shown great potential in enhancing applications like biological/chemical sensing, light harvesting and energy transfer, and optical/quantum computing. Therefore, an extensive effort has been vested in optimizing plasmonic systems and exploiting their field enhancement properties. Super-resolution imaging with quantum dots (QDs) is a promising method to probe plasmonic near-fields but is hindered by the distortion of the QD radiation pattern. Here, we investigate the interaction between QDs and "L-shaped" gold nanoantennas and demonstrate both theoretically and experimentally that this strong interaction can induce polarization-dependent modifications to the apparent QD emission intensity, polarization, and localization. Based on FDTD simulations and polarization-modulated single-molecule microscopy, we show that the displacement of the emitter's localization is due to the position-dependent interference between the emitter and the induced dipole, and can be up to 100 nm. Our results help pave a pathway for higher precision plasmonic near-field mapping and its underlying applications.

Single-Molecule Blinking Fluorescence Enhancement by Surface Plasmon-Coupled Emission-Based Substrates for Single-Molecule Localization Imaging

Surface plasmon-coupled emission (SPCE) substrates to enhance the blinking fluorescence of spontaneously blinking fluorophores in single-molecule localization microscopy (SMLM) were fabricated to reduce the excitation power density requirement and reveal the distribution of fluorophore-labeled proteins on a plasma membrane with nanoscale-level resolution. The systemic investigation of the contribution of local field enhancement, modified quantum yield, and emission coupling yield through glass coverslip substrates coated with metal layers of different thicknesses revealed that the silver-layer substrate with a thickness of 44 nm produces the highest SPCE fluorescence in spontaneously blinking fluorophores, and it has a highly directional SPCE fluorescence, which helps improve the detection efficiency. Moreover, the uniform and surface-enhanced field created on the substrate surface is beneficial for fluorescence background reduction in single fluorophore detection and localization, as well as for revealing the real position of fluorophores. Consequently, compared with a glass coverslip substrate, the presented SPCE substrate demonstrated a fluorescence enhancement of 480% and an increase in blinking events from a single spontaneously blinking fluorophore; moreover, the required excitation power density for SMLM imaging was significantly reduced to 23 W cm^-2 for visualizing the distribution of epidermal growth factor receptors (EGFRs) on the basal plasma membrane of A549 lung cancer cells with a localization precision of 19 ± 7 nm. Finally, the fluorophore-labeled EGFRs on the basal plasma membrane in the presence of PIKfyve-specific inhibitor treatment were explored using SPCE-SMLM imaging; the results revealed a distinct reduction in the density of localization events because of a decrease in EGFR abundance at the plasma membranes of the cells.

Imaging and Localization of Single Emitters near Plasmonic Particles of Different Size, Shape, and Material

Colloidal plasmonic materials are increasingly used in biosensing and catalysis, which has sparked the use of super-resolution localization microscopy to visualize processes at the interface of the particles. We quantify the effect of particle-emitter coupling on super-resolution localization accuracy by simulating the point spread function (PSF) of single emitters near a plasmonic nanoparticle. Using a computationally inexpensive boundary element method, we investigate a broad range of conditions allowing us to compare the simulated localization accuracy to reported experimental results. We identify regimes where the PSF is not Gaussian anymore, resulting in large mislocalizations due to the appearance of multilobed PSFs. Such exotic PSFs occur when near-field excitation of quadrupole plasmons is efficient but unexpectedly also occur for large particle-emitter spacing where the coherent emission from the particle and emitter results in anisotropic emission patterns. We provide guidelines to enable faithful localization microscopy near colloidal plasmonic materials, which indicate that simply decreasing the coupling between particle and molecule is not sufficient for faithful super-resolution imaging.

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.

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.

Super-resolution Imaging of Energy Transfer by Intensity-Based STED-FRET

Förster resonance energy transfer (FRET) imaging methods provide unique insight into the spatial distribution of energy transfer and (bio)molecular interaction events, though they deliver average information for an ensemble of events included in a diffraction-limited volume. Coupling super-resolution fluorescence microscopy and FRET has been a challenging and elusive task. Here, we present STED-FRET, a method of general applicability to obtain super-resolved energy transfer images. In addition to higher spatial resolution, STED-FRET provides a more accurate quantification of interaction and has the capacity of suppressing contributions of noninteracting partners, which are otherwise masked by averaging in conventional imaging. The method capabilities were first demonstrated on DNA-origami model systems, verified on uniformly double-labeled microtubules, and then utilized to image biomolecular interactions in the membrane-associated periodic skeleton (MPS) of neurons.

Toward Sub-Diffraction Imaging of Single-DNA Molecule Sensors Based on Stochastic Switching Localization Microscopy

The natural characteristics of deoxyribonucleic acid (DNA) enable its advanced applications in nanotechnology as a special tool that can be detected by high-resolution imaging with precise localization. Super-resolution (SR) microscopy enables the examination of nanoscale molecules beyond the diffraction limit. With the development of SR microscopy methods, DNA nanostructures can now be optically assessed. Using the specific binding of fluorophores with their target molecules, advanced single-molecule localization microscopy (SMLM) has been expanded into different fields, allowing wide-range detection at the single-molecule level. This review discusses the recent progress in the SR imaging of DNA nano-objects using SMLM techniques, such as direct stochastic optical reconstruction microscopy, binding-activated localization microscopy, and point accumulation for imaging nanoscale topography. Furthermore, we discuss their advantages and limitations, present applications, and future perspectives.

Isolating strong nanoantenna-molecule interactions by ensemble-level single-molecule detection

Traditionally, the nanoscale interaction between single photon emitters and plasmonic nanostructures is studied by relying on deterministic, near-perfect, nanoscale-control, either top-down or bottom-up. However, these approaches are ultra-low throughput thus rendering systematic studies difficult and time-consuming. Here, we show a highly parallelised far-field tactic, combining multiplexed super-resolution fluorescence localization microscopy and data-driven statistical analysis, to study near-field interactions between gold nanorods and single molecules, even at bulk concentrations. We demonstrate that ensemble-level single molecule detection allows separating individual emitters according to their coupling strength with tailored resonant structures, which ultimately permits the reconstruction of super-resolved 2D interaction maps around individual nanoantennas.

Nanoscopy through a plasmonic nanolens

Imaging of single to a few molecules has received much recent interest. While superresolution microscopies access subdiffraction resolution, they do not work for plasmonic hot spots due to the loss of positional information that results from plasmonic coupling. Here, we show how to reconstruct the spatial locations of molecules within a plasmonic hot spot with 1-nm precision. We use a plasmonic nanoball lens to demonstrate that plasmonic nanocavities can be used simultaneously as a nanoscopic and spectroscopic tool. This work opens up possibilities for studying the behavior of a few to single molecules in plasmonic nanoresonators, while simultaneously tracking their movements and spectral features. Our plasmonic nanolens is useful for nanosensing, nanochemistry, and biofunctional imaging.

Plasmonics now delivers sensors capable of detecting single molecules. The emission enhancements and nanometer-scale optical confinement achieved by these metallic nanostructures vastly increase spectroscopic sensitivity, enabling real-time tracking. However, the interaction of light with such nanostructures typically loses all information about the spatial location of molecules within a plasmonic hot spot. Here, we show that ultrathin plasmonic nanogaps support complete mode sets which strongly influence the far-field emission patterns of embedded emitters and allow the reconstruction of dipole positions with 1-nm precision. Emitters in different locations radiate spots, rings, and askew halo images, arising from interference of 2 radiating antenna modes differently coupling light out of the nanogap, highlighting the imaging potential of these plasmonic “crystal balls.” Emitters at the center are now found to live indefinitely, because they radiate so rapidly.

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.

Modeling Surface-Enhanced Spectroscopy With Perturbation Theory

Theoretical modeling of surface-enhanced Raman scattering (SERS) is of central importance for unraveling the interplay of underlying processes and a predictive design of SERS substrates. In this work we model the plasmonic enhancement mechanism of SERS with perturbation theory. We consider the excitation of plasmonic modes as an integral part of the Raman process and model SERS as higher-order Raman scattering. Additional resonances appear in the Raman cross section which correspond to the excitation of plasmons at the wavelengths of the incident and the Raman-scattered light. The analytic expression for the Raman cross section can be used to explain the outcome of resonance Raman measurements on SERS analytes as we demonstrate by comparison to experimental data. We also implement the theory to calculate the optical absorption cross section of plasmonic nanoparticles. From a comparison to experimental cross sections, we show that the coupling matrix elements need to be renormalized by a factor that accounts for the depolarization by the bound electrons and interband transitions in order to obtain the correct magnitude. With model calculations we demonstrate that interference of different scattering channels is key to understand the excitation energy dependence of the SERS enhancement for enhancement factors below 103.

Wavelength-scale errors in optical localization due to spin-orbit coupling of light

Far-field optical imaging techniques allow the determination of the position of point-like emitters and scatterers [1-3]. Although the optical wavelength sets a fundamental limit to the image resolution of unknown objects, the position of an individual emitter can in principle be estimated from the image with arbitrary precision. This is used for example in the determination of stars position [4] or in optical super-resolution microscopy [5]. Furthermore, precise position determination is an experimental prerequisite for the manipulation and measurement of individual quantum systems, such as atoms, ions, and solid-state-based quantum emitters [6-8]. Here we demonstrate that spin-orbit coupling of light in the emission of elliptically polarized emitters can lead to systematic, wavelength-scale errors in the estimation of the emitters position. Imaging a single trapped atom as well as a single sub-wavelength-diameter gold nanoparticle, we demonstrate a shift between the emitters measured and actual positions which is comparable to the optical wavelength. For certain settings, the expected shift can become arbitrarily large. Beyond optical imaging techniques, our findings could be relevant for the localization of objects using any type of wave that carries orbital angular momentum relative to the emitters position with a component orthogonal to the direction of observation.

Sharpening emitter localization in front of a tuned mirror

Single-molecule localization microscopy (SMLM) aims for maximized precision and a high signal-to-noise ratio¹. Both features can be provided by placing the emitter in front of a metal-dielectric nanocoating that acts as a tuned mirror^2-4. Here, we demonstrate that a higher photon yield at a lower background on biocompatible metal-dielectric nanocoatings substantially improves SMLM performance and increases the localization precision by up to a factor of two. The resolution improvement relies solely on easy-to-fabricate nanocoatings on standard glass coverslips and is spectrally and spatially tunable by the layer design and wavelength, as experimentally demonstrated for dual-color SMLM in cells.

Enhancing the blinking fluorescence of single-molecule localization imaging by using a surface-plasmon-polariton-enhanced substrate

Super-resolution imaging based on single-molecule localization microscopy combined with the surface plasmon polariton (SPP)-enhanced fluorescence of spontaneously blinking fluorophores was demonstrated to visualize the nanoscale-level positioning information of cell-adhesion-associated proteins. Glass substrates with a deposited silver layer were utilized to induce a SPP-enhanced field on the silver surface and significantly strengthen the fluorescence signals of the fluorophores by more than 300%. The illumination power density for localization imaging at a spatial resolution of 25 ± 11 nm was 31.6 W cm-2. This low illumination power density will facilitate the reduction of phototoxicity of the biospecimens for single-molecule localization imaging. The proposed strategy provides a uniform distribution of the SPP-enhanced field on the silver surface, enabling visualization of the spatial distribution of labeled proteins without interference caused by the enhanced field distribution.

Parallel mapping of optical near-field interactions by molecular motor-driven quantum dots

In the vicinity of metallic nanostructures, absorption and emission rates of optical emitters can be modulated by several orders of magnitude^1,2. Control of such near-field light-matter interaction is essential for applications in biosensing³, light harvesting⁴ and quantum communication^5,6 and requires precise mapping of optical near-field interactions, for which single-emitter probes are promising candidates^7-11. However, currently available techniques are limited in terms of throughput, resolution and/or non-invasiveness. Here, we present an approach for the parallel mapping of optical near-field interactions with a resolution of <5 nm using surface-bound motor proteins to transport microtubules carrying single emitters (quantum dots). The deterministic motion of the quantum dots allows for the interpolation of their tracked positions, resulting in an increased spatial resolution and a suppression of localization artefacts. We apply this method to map the near-field distribution of nanoslits engraved into gold layers and find an excellent agreement with finite-difference time-domain simulations. Our technique can be readily applied to a variety of surfaces for scalable, nanometre-resolved and artefact-free near-field mapping using conventional wide-field microscopes.

Imaging Plasmon Hybridization of Fano Resonances via Hot-Electron-Mediated Absorption Mapping

The inhibition of radiative losses in dark plasmon modes allows storing electromagnetic energy more efficiently than in far-field excitable bright-plasmon modes. As such, processes benefiting from the enhanced absorption of light in plasmonic materials could also take profit of dark plasmon modes to boost and control nanoscale energy collection, storage, and transfer. We experimentally probe this process by imaging with nanoscale precision the hot-electron driven desorption of thiolated molecules from the surface of gold Fano nanostructures, investigating the effect of wavelength and polarization of the incident light. Spatially resolved absorption maps allow us to show the contribution of each element of the nanoantenna in the hot-electron driven process and their interplay in exciting a dark plasmon mode. Plasmon-mode engineering allows control of nanoscale reactivity and offers a route to further enhance and manipulate hot-electron driven chemical reactions and energy-conversion and transfer at the nanoscale.

Chemical and Biological Sensing Using Hybridization Chain Reaction

Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.

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.

Nanoscale Control of Molecular Self-Assembly Induced by Plasmonic Hot-Electron Dynamics

Self-assembly processes allow designing and creating complex nanostructures using molecules as building blocks and surfaces as scaffolds. This autonomous driven construction is possible due to a complex thermodynamic balance of molecule-surface interactions. As such, nanoscale guidance and control over this process is hard to achieve. Here we use the highly localized light-to-chemical-energy conversion of plasmonic materials to spatially cleave Au-S bonds on predetermined locations within a single nanoparticle, enabling a high degree of control over this archetypal system for molecular self-assembly. Our method offers nanoscale precision and high-throughput light-induced tailoring of the surface chemistry of individual and packed nanosized metallic structures by simply varying wavelength and polarization of the incident light. Assisted by single-molecule super-resolution fluorescence microscopy, we image, quantify, and shed light onto the plasmon-induced desorption mechanism. Our results point toward localized distribution of hot electrons, contrary to uniformly distributed lattice heating, as the mechanism inducing Au-S bond breaking. We demonstrate that plasmon-induced photodesorption enables subdiffraction and even subparticle multiplexing. Finally, we explore possible routes to further exploit these concepts for the selective positioning of nanomaterials and the sorting and purification of colloidal nanoparticles.

All-Optical Imaging of Gold Nanoparticle Geometry Using Super-Resolution Microscopy

We demonstrate the all-optical reconstruction of gold nanoparticle geometry using super-resolution microscopy. We employ DNA-PAINT to get exquisite control over the (un)binding kinetics by the number of complementary bases and salt concentration, leading to localization accuracies of ∼5 nm. We employ a dye with an emission spectrum strongly blue-shifted from the plasmon resonance to minimize mislocalization due to plasmon-fluorophore coupling. We correlate the all-optical reconstructions with atomic force microscopy images and find that reconstructed dimensions deviate by no more than ∼10%. Numerical modeling shows that this deviation is determined by the number of events per particle, and the signal-to-background ratio in our measurement. We further find good agreement between the reconstructed orientation and aspect ratio of the particles and single-particle scattering spectroscopy. This method may provide an approach to all-optically image the geometry of single particles in confined spaces such as microfluidic circuits and biological cells, where access with electron beams or tip-based probes is prohibited.

Using DNA origami nanorulers as traceable distance measurement standards and nanoscopic benchmark structures

In recent years, DNA origami nanorulers for superresolution (SR) fluorescence microscopy have been developed from fundamental proof-of-principle experiments to commercially available test structures. The self-assembled nanostructures allow placing a defined number of fluorescent dye molecules in defined geometries in the nanometer range. Besides the unprecedented control over matter on the nanoscale, robust DNA origami nanorulers are reproducibly obtained in high yields. The distances between their fluorescent marks can be easily analysed yielding intermark distance histograms from many identical structures. Thus, DNA origami nanorulers have become excellent reference and training structures for superresolution microscopy. In this work, we go one step further and develop a calibration process for the measured distances between the fluorescent marks on DNA origami nanorulers. The superresolution technique DNA-PAINT is used to achieve nanometrological traceability of nanoruler distances following the guide to the expression of uncertainty in measurement (GUM). We further show two examples how these nanorulers are used to evaluate the performance of TIRF microscopes that are capable of single-molecule localization microscopy (SMLM).

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.

Super-Resolving the Actual Position of Single Fluorescent Molecules Coupled to a Plasmonic Nanoantenna

Plasmonic nanoparticles (NPs) enhance the radiative decay rate of adjacent dyes and can significantly increase fluorescence intensity for improved spectroscopy. However, the NP nanoantenna complicates super-resolution imaging by introducing a mislocalization between the emitter position and its super-resolved emission position. The mislocalization magnitude depends strongly on the dye/NP coupling geometry. It is therefore crucial to quantify mislocalization to recover the actual emitter position in a coupled system. Here, we super-resolve in two and three dimensions the distance-dependent emission mislocalization of single fluorescent molecules coupled to gold NPs with precise distance tuning via double-stranded DNA. We develop an analytical framework to uncover detailed spatial information when direct 3D imaging is not accessible. Overall, we demonstrate that by taking measurements on a single, well-defined, and symmetric dye/NP assembly and by accounting explicitly for artifacts from super-resolution imaging, we can measure the true nanophotonic mislocalization. We measure up to 50 nm mislocalizations and show that smaller separation distances lead to larger mislocalizations, also verified by electromagnetic calculations. Overall, by quantifying the distance-dependent mislocalization shift in this gold NP/dye coupled system, we show that the actual physical position of a coupled single emitter can be recovered.

Modeling super-resolution SERS using a T-matrix method to elucidate molecule-nanoparticle coupling and the origins of localization errors

A computational method to model diffraction-limited images from super-resolution surface-enhanced Raman scattering microscopy is introduced. Despite significant experimental progress in plasmon-based super-resolution imaging, theoretical predictions of the diffraction limited images remain a challenge. The method is used to calculate localization errors and image intensities for a single spherical gold nanoparticle-molecule system. The light scattering is calculated using a modification of generalized Mie (T-matrix) theory with a point dipole source and diffraction limited images are calculated using vectorial diffraction theory. The calculation produces the multipole expansion for each emitter and the coherent superposition of all fields. Imaging the constituent fields in addition to the total field provides new insight into the strong coupling between the molecule and the nanoparticle. Regardless of whether the molecular dipole moment is oriented parallel or perpendicular to the nanoparticle surface, the anisotropic excitation distorts the center of the nanoparticle as measured by the point spread function by approximately fifty percent of the particle radius toward to the molecule. Inspection of the nanoparticle multipoles reveals that distortion arises from a weak quadrupole resonance interfering with the dipole field in the nanoparticle. When the nanoparticle-molecule fields are in-phase, the distorted nanoparticle field dominates the observed image. When out-of-phase, the nanoparticle and molecule are of comparable intensity and interference between the two emitters dominates the observed image. The method is also applied to different wavelengths and particle radii. At off-resonant wavelengths, the method predicts images closer to the molecule not because of relative intensities but because of greater distortion in the nanoparticle. The method is a promising approach to improving the understanding of plasmon-enhanced super-resolution experiments.