Single-molecule detection at high concentrations with optical aperture nanoantennas

Bio-Inspired Nanomembranes as Building Blocks for Nanophotonics, Plasmonics and Metamaterials

Nanomembranes are the most widespread building block of life, as they encompass cell and organelle walls. Their synthetic counterparts can be described as freestanding or free-floating structures thinner than 100 nm, down to monatomic/monomolecular thickness and with giant lateral aspect ratios. The structural confinement to quasi-2D sheets causes a multitude of unexpected and often counterintuitive properties. This has resulted in synthetic nanomembranes transiting from a mere scientific curiosity to a position where novel applications are emerging at an ever-accelerating pace. Among wide fields where their use has proven itself most fruitful are nano-optics and nanophotonics. However, the authors are unaware of a review covering the nanomembrane use in these important fields. Here, we present an attempt to survey the state of the art of nanomembranes in nanophotonics, including photonic crystals, plasmonics, metasurfaces, and nanoantennas, with an accent on some advancements that appeared within the last few years. Unlimited by the Nature toolbox, we can utilize a practically infinite number of available materials and methods and reach numerous properties not met in biological membranes. Thus, nanomembranes in nano-optics can be described as real metastructures, exceeding the known materials and opening pathways to a wide variety of novel functionalities.

Gold Ion Beam Milled Gold Zero-Mode Waveguides

Zero-mode waveguides (ZMWs) are widely used in single molecule fluorescence microscopy for their enhancement of emitted light and the ability to study samples at physiological concentrations. ZMWs are typically produced using photo or electron beam lithography. We report a new method of ZMW production using focused ion beam (FIB) milling with gold ions. We demonstrate that ion-milled gold ZMWs with 200 nm apertures exhibit similar plasmon-enhanced fluorescence seen with ZMWs fabricated with traditional techniques such as electron beam lithography.

Spontaneous Emission Enhancement by a Rectangular-Aperture Optical Nanoantenna: An Intuitive Semi-Analytical Model of Surface Plasmon Polaritons

The spontaneous-emission enhancement effect of a single metallic rectangular-aperture optical nanoantenna on a SiO2 substrate was investigated theoretically. By considering the excitation and multiple scattering of surface plasmon polaritons (SPPs) in the aperture, an intuitive and comprehensive SPP model was established. The model can comprehensively predict the total spontaneous emission rate, the radiative emission rate and the angular distribution of the far-field emission of a point source in the aperture. Two phase-matching conditions are derived from the model for predicting the resonance and show that the spontaneous-emission enhancement by the antenna comes from the Fabry–Perot resonance of the SPP in the aperture. In addition, when scanning the position of the point source and the aperture length, the SPP model does not need to repeatedly solve the Maxwell’s equations, which shows a superior computational efficiency compared to the full-wave numerical method.

Fast interaction dynamics of G-quadruplex and RGG-rich peptides unveiled in zero-mode waveguides

G-quadruplexes (GQs), a non-canonical form of DNA, are receiving a huge interest as target sites for potential applications in antiviral and anticancer drug treatments. The biological functions of GQs can be controlled by specifically binding proteins known as GQs binding proteins. Some of the GQs binding proteins contain an arginine and glycine-rich sequence known as RGG peptide. Despite the important role of RGG, the GQs-RGG interaction remains poorly understood. By single molecule measurements, the interaction dynamics can be determined in principle. However, the RGG-GQs interaction occurs at micromolar concentrations, making conventional single-molecule experiments impossible with a diffraction-limited confocal microscope. Here, we use a 120 nm zero-mode waveguide (ZMW) nanoaperture to overcome the diffraction limit. The combination of dual-color fluorescence cross-correlation spectroscopy (FCCS) with FRET is used to unveil the interaction dynamics and measure the association and dissociation rates. Our data show that the RGG-GQs interaction is predominantly driven by electrostatics but that a specific affinity between the RGG sequence and the GQs structure is preserved. The single molecule approach at micromolar concentration is the key to improve our understanding of GQs function and develop its therapeutic applications by screening a large library of GQs-targeting peptides and proteins.

DNA Manipulation and Single-Molecule Imaging

DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.

Zero-mode waveguides can be made better: fluorescence enhancement with rectangular aluminum nanoapertures from the visible to the deep ultraviolet

Nanoapertures milled in metallic films called zero-mode waveguides (ZMWs) overcome the limitations of classical confocal microscopes by enabling single molecule analysis at micromolar concentrations with improved fluorescence brightness. While the ZMWs have found many applications in single molecule fluorescence studies, their shape has been mainly limited to be circular. Owing to the large parameter space to explore and the lack of guidelines, earlier attempts using more elaborate shapes have led to unclear conclusions whether or not the performance was improved as compared to a circular ZMW. Here, we comparatively analyze the performance of rectangular-shaped nanoapertures milled in aluminum to enhance the fluorescence emission rate of single molecules from the near infrared to the deep ultraviolet. Our new design is based on rational principles taking maximum advantage of the laser linear polarization. While the long edge of the nanorectangle is set to meet the cut-off size for the propagation of light into the nanoaperture, the short edge is reduced to 30 nm to accelerate the photodynamics while maintaining bright fluorescence rates. Our results show that both in the red and in the ultraviolet, the nanorectangles provide 50% brighter photon count rates as compared to the best performing circular ZMWs and achieve fluorescence lifetimes shorter than 300 ps. These findings can be readily used to improve the performance of ZMWs, especially for fast biomolecular dynamics, bright single-photon sources, and ultraviolet plasmonics.

Mixed metal zero-mode guides (ZMWs) for tunable fluorescence enhancement

Zero-mode waveguides (ZMWs) are capable of modifying fluorescence emission through interactions with surface plasmon modes leading to either plasmon-enhanced fluorescence or quenching. Enhancement requires spectral overlap of the plasmon modes with the absorption or emission of the fluorophore. Thus, enhancement is limited to fluorophores in resonance with metals (e.g. Al, Au, Ag) used for ZMWs. The ability to tune interactions to match a wider range of fluorophores across the visible spectra would significantly extend the utility of ZMWs. We fabricated ZMWs composed of aluminum and gold individually and also in mixtures of three different ratios, (Al : Au; 75 : 25, 50 : 50, 25 : 75). We characterized the effect of mixed-metal ZMWs on single-molecule emission for a range fluorophores across the visible spectrum. Mixed metal ZMWs exhibited a shift in the spectral range where they exhibited the maximum fluorescence enhancement allowing us to match the emission of fluorophores that were nonresonant with single metal ZMWs. We also compared the effect of mixed-metal ZMWs on the photophysical properties of fluorescent molecules due to metal-molecule interactions. We quantified changes in fluorescence lifetimes and photostability that were dependent on the ratio of Au and Al. Tuning the enhancement properties of ZMWs by changing the ratio of Au and Al allowed us to match the fluorescence of fluorophores that emit in different regions of the visible spectrum.

Surface passivation of zero-mode waveguide nanostructures: benchmarking protocols and fluorescent labels

Zero mode waveguide (ZMW) nanoapertures efficiently confine the light down to the nanometer scale and overcome the diffraction limit in single molecule fluorescence analysis. However, unwanted adhesion of the fluorescent molecules on the ZMW surface can severely hamper the experiments. Therefore a proper surface passivation is required for ZMWs, but information is currently lacking on both the nature of the adhesion phenomenon and the optimization of the different passivation protocols. Here we monitor the influence of the fluorescent dye (Alexa Fluor 546 and 647, Atto 550 and 647N) on the non-specific adhesion of double stranded DNA molecule. We show that the nonspecific adhesion of DNA double strands onto the ZMW surface is directly mediated by the organic fluorescent dye being used, as Atto 550 and Atto 647N show a pronounced tendency to adhere to the ZMW while the Alexa Fluor 546 and 647 are remarkably free of this effect. Despite the small size of the fluorescent label, the surface charge and hydrophobicity of the dye appear to play a key role in promoting the DNA affinity for the ZMW surface. Next, different surface passivation methods (bovine serum albumin BSA, polyethylene glycol PEG, polyvinylphosphonic acid PVPA) are quantitatively benchmarked by fluorescence correlation spectroscopy to determine the most efficient approaches to prevent the adsorption of Atto 647N labeled DNA. Protocols using PVPA and PEG-silane of 1000 Da molar mass are found to drastically avoid the non-specific adsorption into ZMWs. Optimizing both the choice of the fluorescent dye and the surface passivation protocol are highly significant to expand the use of ZMWs for single molecule fluorescence applications.

Photothermal Effect in Plasmonic Nanotip for LSPR Sensing

The influence of heat generation on the conventional process of LSPR based sensing has not been explored thus far. Therefore, a need exists to draw attention toward the heat generation issue during LSPR sensing as it may affect the refractive index of the analyte, leading to incorrect sensory conclusions. This manuscript addresses the connection between the photo-thermal effect and LSPR. We numerically analyzed the heat performance of a gold cladded nanotip. The numerical results predict a change in the micro-scale temperature in the microenvironment near the nanotip. These numerical results predict a temperature increase of more than 20 K near the apex of the nanotip, which depends on numerous factors including the input optical power and the diameter of the fiber. We analytically show that this change in the temperature influences a change in the refractive index of the microenvironment in the vicinity of the nanotip. In accordance with our numerical and analytical findings, we experimentally show an LSPR shift induced by a change in the input power of the source. We believe that our work will bring the importance of temperature dependence in nanotip based LSPR sensing to the fore.

Nanoradiator-Mediated Deterministic Opto-Thermoelectric Manipulation

Optical manipulation of colloidal nanoparticles and molecules is significant in numerous fields. Opto-thermoelectric nanotweezers exploiting multiple coupling among light, heat, and electric fields enables the low-power optical trapping of nanoparticles on a plasmonic substrate. However, the management of light-to-heat conversion for the versatile and precise manipulation of nanoparticles is still elusive. Herein, we explore the opto-thermoelectric trapping at plasmonic antennas that serve as optothermal nanoradiators to achieve the low-power (∼0.08 mW/μm2) and deterministic manipulation of nanoparticles. Specifically, precise optical manipulation of nanoparticles is achieved via optical control of the subwavelength thermal hot spots. We employ a femtosecond laser beam to further improve the heat localization and the precise trapping of single ∼30 nm semiconductor quantum dots at the antennas where the plasmon-exciton coupling can be tuned. With its low-power, precise, and versatile particle control, the opto-thermoelectric manipulation can have applications in photonics, life sciences, and colloidal sciences.

Plasmonic zero mode waveguide for highly confined and enhanced fluorescence emission

We fabricate a plasmonic nanoslot that is capable of performing enhanced single molecule detection at 10 μM concentrations. The nanoslot combines the tiny detection volume of a zero-mode waveguide and the field enhancement of a plasmonic nanohole. The nanoslot is fabricated on a bi-metallic film formed by the sequential deposition of gold and aluminum on a transparent substrate. Simulations of the structure yield an average near-field intensity enhancement of two orders of magnitude at its resonant frequency. Experimentally, we measure the fluorescence stemming from the nanoslot and compare it with that of a standard aluminum zero-mode waveguide. We also compare the detection volume for both structures. We observe that while both structures have a similar detection volume, the nanoslot yields a 25-fold fluorescence enhancement.

Understanding quantum emitters in plasmonic nanocavities with conformal transformation: Purcell enhancement and forces

Nanogaps supporting cavity plasmonic modes with unprecedented small mode volume are attractive platforms for tailoring the properties of light-matter interactions at the nanoscale and revealing new physics. Hitherto, there is a concerning lack of analytical solutions to divide the complex interactions into their different underlying mechanisms to gain a better understanding that can foster enhanced designs. Bowtie apertures are viewed as an effective and appealing nanocavity and are studied here within the analytical frame of conformal transformation. We show how the non-radiative Purcell enhancement of a quantum emitter within the bowtie nanocavity depends strongly not only on the geometry of the nanocavity, but also on the position and orientation of the emitter. For a 20 nm diameter (∅ 20 nm) bowtie nanocavity, we report a change of up to two orders of magnitude in the maximum non-radiative Purcell enhancement and a shift in its peak wavelength from green to infra-red. The changes are tracked down to the overlap between the emitter field and the gap plasmon mode field distribution. This analysis also enables us to understand the self-induced trapping potential of a colloidal quantum dot inside the nanocavity. Since transformations can be cascaded, the technique introduced in this work can also be applied to a wide range of nanocavities found in the literature.

Zero-Mode Waveguide Nanophotonic Structures for Single Molecule Characterization

Single-molecule characterization has become a crucial research tool in the chemical and life sciences, but limitations, such as limited concentration range, inability to control molecular distributions in space, and intrinsic phenomena, such as photobleaching, present significant challenges. Recent developments in non-classical optics and nanophotonics offer promising routes to mitigating these restrictions, such that even low affinity (K D ~ mM) biomolecular interactions can be studied. Here we introduce and review specific nanophotonic devices used to support single molecule studies. Optical nanostructures, such as zero-mode waveguides (ZMWs), are usually fabricated in thin gold or aluminum films and serve to confine the observation volume of optical microspectroscopy to attoliter to zeptoliter volumes. These simple nanostructures allow individual molecules to be isolated for optical and electrochemical analysis, even when the molecules of interest are present at high concentration (μM - mM) in bulk solution. Arrays of ZMWs may be combined with optical probes such as single molecule fluorescence, single molecule fluorescence resonance energy transfer (smFRET), and fluorescence correlation spectroscopy (FCS) for distributed analysis of large numbers of single-molecule reactions or binding events in parallel. Furthermore, ZMWs may be used as multifunctional devices, for example by combining optical and electrochemical functions in a single discrete architecture to achieve electrochemical ZMWs (E-ZMW). In this review, we will describe the optical properties, fabrication, and applications of ZMWs for single-molecule studies, as well as the integration of ZMWs into systems for chemical and biochemical analysis.

Single-Molecule Plasmon Sensing: Current Status and Future Prospects

Single-molecule detection has long relied on fluorescent labeling with high quantum-yield fluorophores. Plasmon-enhanced detection circumvents the need for labeling by allowing direct optical detection of weakly emitting and completely nonfluorescent species. This review focuses on recent advances in single molecule detection using plasmonic metal nanostructures as a sensing platform, particularly using a single particle-single molecule approach. In the past decade two mechanisms for plasmon-enhanced single-molecule detection have been demonstrated: (1) by plasmonically enhancing the emission of weakly fluorescent biomolecules, or (2) by monitoring shifts of the plasmon resonance induced by single-molecule interactions. We begin with a motivation regarding the importance of single molecule detection, and advantages plasmonic detection offers. We describe both detection mechanisms and discuss challenges and potential solutions. We finalize by highlighting the exciting possibilities in analytical chemistry and medical diagnostics.