Nanoaperture fabrication via colloidal lithography for single molecule fluorescence analysis

Large-Scale Formation of a Close-Packed Monolayer of Spheres Using Different Colloidal Lithography Techniques

The possibility of using colloidal lithography at the industrial level depends on the ability to form defect-free coatings over large areas. The spin-coating method has not yet shown acceptable results, but a more detailed studying of the regularities of this process may improve the quality of masks. The Langmuir-Blodgett method is expected to be the most preferable for forming high-quality large-scale monolayers. Real-time controlling the surface pressure of the monolayer can allow to obtain close-packed arrays with long-range order. In this work, to develop the spin-coating technology, the influence of technological parameters (spin-coating speed and time, concentrations of components in suspension) on the substrate coverage area with a monolayer of polystyrene spheres (1.25 μm) was studied. An original automated Langmuir-Blodgett system was developed to study the influence of the monolayer surface pressure on its quality using polystyrene spheres (1.25, 1.8, 2.1 μm). The developed spin-coating technology resulted in a record coverage area (90%) of Si substrate (76 mm) and a defect-free hexagonally ordered domain area of 500 μm2. As a result of the developed Langmuir-Blodgett technique, a close-packed monolayer coating was obtained over the entire substrate area (coverage area 99.5%, defect-free domain area 3000 μm2) without the use of any surfactants.

Heat: A powerful tool for colloidal particle shaping

Colloidal particles of spherical shape are important building blocks for nanotechnological applications. Materials with tailored physical properties can be directly synthesized from self-assembled particles, as is the case for colloidal photonic crystals. In addition, colloidal monolayers and multilayers can be exploited as a mask for the fabrication of complex nanostructures via a colloidal lithography process for applications ranging from optoelectronics to sensing. Several techniques have been adopted to modify the shape of both individual colloidal particles and colloidal masks. Thermal treatment of colloidal particles is an effective route to introduce colloidal particle deformation or to manipulate colloidal masks (i.e. to tune the size of the interstices between colloidal particles) by heating them at elevated temperatures above a certain critical temperature for the particle material. In particular, this type of morphological manipulation based on thermal treatments has been extensively applied to polymer particles. Nonetheless, interesting shaping effects have been observed also in inorganic materials, in particular silica particles. Due to their much less complex implementation and distinctive shaping effects in comparison to dry etching or high energy ion beam irradiation, thermal treatments turn out to be a powerful and competitive tool to induce colloidal particle deformation. In this review, we examine the physicochemical principles and mechanisms of heat-induced shaping as well as its experimental implementation. We also explore its applications, going from tailored masks for colloidal lithography to the fabrication of colloidal assemblies directly useful for their intrinsic optical, thermal and mechanical properties (e.g. thermal switches) and even to the synthesis of supraparticles and anisotropic particles, such as doublets.

Hexagonal Plasmonic Arrays for High-Throughput Multicolor Single-Molecule Studies

Nanophotonic biosensors offer exceptional sensitivity in the presence of strong background signals by enhancing and confining light in subwavelength volumes. In the field of nanophotonic biosensors, antenna-in-box (AiB) designs consisting of a nanoantenna within a nanoaperture have demonstrated remarkable single-molecule fluorescence detection sensitivities under physiologically relevant conditions. However, their full potential has not yet been exploited as current designs prohibit insightful correlative multicolor single-molecule studies and are limited in terms of throughput. Here, we overcome these constraints by introducing aluminum-based hexagonal close-packed AiB (HCP-AiB) arrays. Our approach enables the parallel readout of over 1000 HCP-AiBs with multicolor single-molecule sensitivity up to micromolar concentrations using an alternating three-color excitation scheme and epi-fluorescence detection. Notably, the high-density HCP-AiB arrays not only enable high-throughput studies at micromolar concentrations but also offer high single-molecule detection probabilities in the nanomolar range. We demonstrate that robust and alignment-free correlative multicolor studies are possible using optical fiducial markers even when imaging in the low millisecond range. These advancements pave the way for the use of HCP-AiB arrays as biosensor architectures for high-throughput multicolor studies on single-molecule dynamics.

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.

Enhancing Single-Molecule Fluorescence Spectroscopy with Simple and Robust Hybrid Nanoapertures

Plasmonic nanoapertures have found exciting applications in optical sensing, spectroscopy, imaging, and nanomanipulation. The subdiffraction optical field localization, reduced detection volume (~attoliters), and background-free operation make them particularly attractive for single-particle and single-molecule studies. However, in contrast to the high field enhancements by traditional "nanoantenna"-based structures, small field enhancement in conventional nanoapertures results in weak light-matter interactions and thus small enhancement of spectroscopic signals (such as fluorescence and Raman signals) of the analytes interacting with the nanoapertures. In this work, we propose a hybrid nanoaperture design termed "gold-nanoislands-embedded nanoaperture" (AuNIs-e-NA), which provides multiple electromagnetic "hotspots" within the nanoaperture to achieve field enhancements of up to 4000. The AuNIs-e-NA was able to improve the fluorescence signals by more than 2 orders of magnitude with respect to a conventional nanoaperture. With simple design and easy fabrication, along with strong signal enhancements and operability over variable light wavelengths and polarizations, the AuNIs-e-NA will serve as a robust platform for surface-enhanced optical sensing, imaging, and spectroscopy.

Recent advances in plasmonic nanocavities for single-molecule spectroscopy

Plasmonic nanocavities are able to engineer and confine electromagnetic fields to subwavelength volumes. In the past decade, they have enabled a large set of applications, in particular for sensing, optical trapping, and the investigation of physical and chemical phenomena at a few or single-molecule levels. This extreme sensitivity is possible thanks to the highly confined local field intensity enhancement, which depends on the geometry of plasmonic nanocavities. Indeed, suitably designed structures providing engineered local optical fields lead to enhanced optical sensing based on different phenomena such as surface enhanced Raman scattering, fluorescence, and Förster resonance energy transfer. In this mini-review, we illustrate the most recent results on plasmonic nanocavities, with specific emphasis on the detection of single molecules.

Single molecule turnover of fluorescent ATP by myosin and actomyosin unveil elusive enzymatic mechanisms

Benefits of single molecule studies of biomolecules include the need for minimal amounts of material and the potential to reveal phenomena hidden in ensembles. However, results from recent single molecule studies of fluorescent ATP turnover by myosin are difficult to reconcile with ensemble studies. We found that key reasons are complexities due to dye photophysics and fluorescent contaminants. After eliminating these, through surface cleaning and use of triple state quenchers and redox agents, the distributions of ATP binding dwell times on myosin are best described by 2 to 3 exponential processes, with and without actin, and with and without the inhibitor para-aminoblebbistatin. Two processes are attributable to ATP turnover by myosin and actomyosin respectively, whereas the remaining process (rate constant 0.2–0.5 s⁻¹) is consistent with non-specific ATP binding to myosin, possibly accelerating ATP transport to the active site. Finally, our study of actin-activated myosin ATP turnover without sliding between actin and myosin reveals heterogeneity in the ATP turnover kinetics consistent with models of isometric contraction.

With fluorescence based-TIRF microspectroscopy, Ušaj et al. unveil mechanistic details about the ATP turnover rates by myosin and actomyosin with enzymatic reaction pathways that were not possible to obtain from ensemble studies. This study could be important to the field of molecular motors.

Compensation of disorder for extraordinary optical transmission effect in nanopore arrays fabricated by nanosphere photolithography

The work considers the effect of extraordinary optical transmission (EOT) in polycrystalline arrays of nanopores fabricated via nanosphere photolithography (NPL). The use of samples with different qualities of polycrystalline structure allows us to reveal the role of disorder for EOT. We propose a phenomenological model which takes the disorder into account in numerical simulations and validate it using experimental data. Due to the NPL flexibility for the structure geometry control, we demonstrate the possiblity to partially compensate the disorder influence on EOT by the nanopore depth adjustments. The proposed experimental and theoretical results are promising to reveal the NPL limits for EOT-based devices and stimulate systematic studies of disorder compensation designs.

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.

Fabrication of Zero Mode Waveguides for High Concentration Single Molecule Microscopy

In single molecule fluorescence enzymology, background fluorescence from labeled substrates in solution often limits fluorophore concentration to pico- to nanomolar ranges, several orders of magnitude less than many physiological ligand concentrations. Optical nanostructures called zero mode waveguides (ZMWs), which are 100-200 nm in diameter apertures fabricated in a thin conducting metal such as aluminum or gold, allow imaging of individual molecules at micromolar concentrations of fluorophores by confining visible light excitation to zeptoliter effective volumes. However, the need for expensive and specialized nanofabrication equipment has precluded the widespread use of ZMWs. Typically, nanostructures such as ZMWs are obtained by direct writing using electron beam lithography, which is sequential and slow. Here, colloidal, or nanosphere, lithography is used as an alternative strategy to create nanometer-scale masks for waveguide fabrication. This report describes the approach in detail, with practical considerations for each phase. The method allows thousands of aluminum or gold ZMWs to be made in parallel, with final waveguide diameters and depths of 100-200 nm. Only common lab equipment and a thermal evaporator for metal deposition are required. By making ZMWs more accessible to the biochemical community, this method can facilitate the study of molecular processes at cellular concentrations and rates.