Fabrication and Characterization of Plasmonic Nanopores with Cavities in the Solid Support

Zero-Mode Waveguide Nanowells for Single-Molecule Detection in Living Cells

Single-molecule fluorescence imaging experiments generally require sub-nanomolar protein concentrations to isolate single protein molecules, which makes such experiments challenging in live cells due to high intracellular protein concentrations. Here, we show that single-molecule observations can be achieved in live cells through a drastic reduction in the observation volume using overmilled zero-mode waveguides (ZMWs- subwavelength-size holes in a metal film). Overmilling of the ZMW in a palladium film creates a nanowell of tunable size in the glass layer below the aperture, which cells can penetrate. We present a thorough theoretical and experimental characterization of the optical properties of these nanowells over a wide range of ZMW diameters and overmilling depths, showing an excellent signal confinement and a 5-fold fluorescence enhancement of fluorescent molecules inside nanowells. ZMW nanowells facilitate live-cell imaging as cells form stable protrusions into the nanowells. Importantly, the nanowells greatly reduce the cytoplasmic background fluorescence, enabling the detection of individual membrane-bound fluorophores in the presence of high cytoplasmic expression levels, which could not be achieved with TIRF microscopy. Zero-mode waveguide nanowells thus provide great potential to study individual proteins in living cells.

Stable trapping of multiple proteins at physiological conditions using nanoscale chambers with macromolecular gates

The possibility to detect and analyze single or few biological molecules is very important for understanding interactions and reaction mechanisms. Ideally, the molecules should be confined to a nanoscale volume so that the observation time by optical methods can be extended. However, it has proven difficult to develop reliable, non-invasive trapping techniques for biomolecules under physiological conditions. Here we present a platform for long-term tether-free (solution phase) trapping of proteins without exposing them to any field gradient forces. We show that a responsive polymer brush can make solid state nanopores switch between a fully open and a fully closed state with respect to proteins, while always allowing the passage of solvent, ions and small molecules. This makes it possible to trap a very high number of proteins (500-1000) inside nanoscale chambers as small as one attoliter, reaching concentrations up to 60 gL-1. Our method is fully compatible with parallelization by imaging arrays of nanochambers. Additionally, we show that enzymatic cascade reactions can be performed with multiple native enzymes under full nanoscale confinement and steady supply of reactants. This platform will greatly extend the possibilities to optically analyze interactions involving multiple proteins, such as the dynamics of oligomerization events.

Pore performance: artificial nanoscale constructs that mimic the biomolecular transport of the nuclear pore complex

The nuclear pore complex is a nanoscale assembly that achieves shuttle-cargo transport of biomolecules: a certain cargo molecule can only pass the barrier if it is attached to a shuttle molecule. In this review we summarize the most important efforts aiming to reproduce this feature in artificial settings. This can be achieved by solid state nanopores that have been functionalized with the most important proteins found in the biological system. Alternatively, the nanopores are chemically modified with synthetic polymers. However, only a few studies have demonstrated a shuttle-cargo transport mechanism and due to cargo leakage, the selectivity is not comparable to that of the biological system. Other recent approaches are based on DNA origami, though biomolecule transport has not yet been studied with these. The highest selectivity has been achieved with macroscopic gels, but they are yet to be scaled down to nano-dimensions. It is concluded that although several interesting studies exist, we are still far from achieving selective and efficient artificial shuttle-cargo transport of biomolecules. Besides being of fundamental interest, such a system could be potentially useful in bioanalytical devices.

Tuning the Thermoresponsive Behavior of Surface-Attached PNIPAM Networks: Varying the Crosslinker Content in SI-ATRP

The synthesis and thermoresponsive properties of surface-attached poly(N-isopropylacrylamide)-co-N,N'-methylene bisacrylamide (PNIPAM-co-MBAM) networks are investigated. The networks are formed via SI-ARGET-ATRP ("grafting-from") on thiol-based initiator-functionalized gold films. This method is reliable, well controlled, fast, and applicable to patterned surfaces (e.g., nanopores) for networks with dry thicknesses >20 nm. Surface-attached PNIPAM-co-MBAM gels are swollen below their volume phase transition temperature but above collapse without complete expulsion of water (retain ∼50 vol %). The swelling/collapse transition is studied using complementary SPR and QCMD techniques. The ratio between swollen and collapsed heights characterizes the thermoresponsive behavior and is shown to not depend on network height but to vary with MBAM content. The higher the proportion of the crosslinker, the lower the magnitude of the phase transition, until all responsiveness is lost at 5 mol % MBAM. The temperature range of the transition is broadened for more crosslinked PNIPAM-co-MBAM gels but remains centered around 32 °C. Upon reswelling, less crosslinked networks display sharp transitions, while for those containing ≥3 mol % MBAM, transitions remain broad. This tunable behavior persists for gels on nanostructured gold surfaces. Investigating PNIPAM-co-MBAM networks on gold plasmonic nanowell arrays is a starting point for expanding their scope as thermo-controlled nanoactuators.

Hollow sphere nickel sulfide nanostructures-based enzyme mimic electrochemical sensor platform for lactic acid in human urine

An enzyme-free electrochemical sensor platform is reported based on hollow sphere structured nickel sulfide (HS-NiS) nanomaterials for the sensitive lactic acid (LA) detection in human urine. Hollow sphere nickel sulfide nanostructures directly grow on the nickel foam (NiF) substrate by using facile and one-step electrochemical deposition strategy towards the electrocatalytic lactic acid oxidation and sensing for the first time. The as-developed nickel sulfide nanostructured electrode (NiF/HS-NiS) has been successfully employed as the enzyme mimic electrode towards the enhanced electrocatalytic oxidation and detection of lactic acid. The NiF/HS-NiS electrode exhibits an excellent electrocatalytic activity and sensing ability with low positive potential (~ 0.52 V vs Ag/AgCl), catalytic current density (~ 1.34 mA), limit of detection (LOD) (0.023 μM), linear range from 0.5 to 88.5 μM with a correlation coefficient of R² = 0.98, sensitivity (0.655 μA μM^-1 cm^-2), and selectivity towards the lactic acid owing to the ascription of high inherent electrical conductivity, large electrochemical active surface area (ECASA), high electrochemical active sites, and strong adsorption ability. The sensors developed in this work demonstrate the selectivity against potential interferences, including uric acid (UA), ascorbic acid (AA), paracetamol (PA), Mg²⁺, Na⁺, and Ca²⁺. Furthermore, the developed sensors show practicability by sensing lactic acid in human urine samples, suggesting that the HS-NiS nanostructures device has promising clinical diagnostic potential. Graphical abstract.

Scalable Fabrication of Quasi-One-Dimensional Gold Nanoribbons for Plasmonic Sensing

Plasmonic nanostructures have a wide range of applications, including chemical and biological sensing. However, the development of techniques to fabricate submicrometer-sized plasmonic structures over large scales remains challenging. We demonstrate a high-throughput, cost-effective approach to fabricate Au nanoribbons via chemical lift-off lithography (CLL). Commercial HD-DVDs were used as large-area templates for CLL. Transparent glass slides were coated with Au/Ti films and functionalized with self-assembled alkanethiolate monolayers. Monolayers were patterned with lines via CLL. The lifted-off, exposed regions of underlying Au were selectively etched into large-area grating-like patterns (200 nm line width; 400 nm pitch; 60 nm height). After removal of the remaining monolayers, a thin In2O3 layer was deposited and the resulting gratings were used as plasmonic sensors. Distinct features in the extinction spectra varied in their responses to refractive index changes in the solution environment with a maximum bulk sensitivity of ∼510 nm/refractive index unit. Sensitivity to local refractive index changes in the near-field was also achieved, as evidenced by real-time tracking of lipid vesicle or protein adsorption. These findings show how CLL provides a simple and economical means to pattern large-area plasmonic nanostructures for applications in optoelectronics and sensing.

Fabrication and Characterization of a Metallic-Dielectric Nanorod Array by Nanosphere Lithography for Plasmonic Sensing Application

In this paper, a periodic metallic–dielectric nanorod array which consists of Si nanorods coated with 30 nm Ag thin film set in a hexagonal configuration is fabricated and characterized. The fabrication procedure is performed by using nanosphere lithography with reactive ion etching, followed by Ag thin-film deposition. The mechanism of the surface and gap plasmon modes supported by the fabricated structure is numerically demonstrated by the three-dimensional finite element method. The measured and simulated absorptance spectra are observed to have a same trend and a qualitative fit. Our fabricated plasmonic sensor shows an average sensitivity of 340.0 nm/RIU when applied to a refractive index sensor ranging from 1.0 to 1.6. The proposed substrates provide a practical plasmonic nanorod-based sensing platform, and the fabrication methods used are technically effective and low-cost.

Nanoplasmonic Sensor Detects Preferential Binding of IRSp53 to Negative Membrane Curvature

Biosensors based on plasmonic nanostructures are widely used in various applications and benefit from numerous operational advantages. One type of application where nanostructured sensors provide unique value in comparison with, for instance, conventional surface plasmon resonance, is investigations of the influence of nanoscale geometry on biomolecular binding events. In this study, we show that plasmonic "nanowells" conformally coated with a continuous lipid bilayer can be used to detect the preferential binding of the insulin receptor tyrosine kinase substrate protein (IRSp53) I-BAR domain to regions of negative surface curvature, i.e., the interior of the nanowells. Two different sensor architectures with and without an additional niobium oxide layer are compared for this purpose. In both cases, curvature preferential binding of IRSp53 (at around 0.025 nm^-1 and higher) can be detected qualitatively. The high refractive index niobium oxide influences the near field distribution and makes the signature for bilayer formation less clear, but the contrast for accumulation at regions of negative curvature is slightly higher. This work shows the first example of analyzing preferential binding of an average-sized and biologically important protein to negative membrane curvature in a label-free manner and in real-time, illustrating a unique application for nanoplasmonic sensors.

Gating Protein Transport in Solid State Nanopores by Single Molecule Recognition

Control of molecular translocation through nanoscale apertures is of great interest for DNA sequencing, biomolecular filters, and new platforms for single molecule analysis. However, methods for controlling the permeability of nanopores are very limited. Here, we show how nanopores functionalized with poly(ethylene glycol) brushes, which fully prevent protein translocation, can be reversibly gated to an "open" state by binding of single IgG antibodies that disrupt the macromolecular barrier. On the basis of surface plasmon resonance data we propose a two-state model describing the antibody-polymer interaction kinetics. Reversibly (weakly) bound antibodies decrease the protein exclusion height while irreversibly (strongly) bound antibodies do not. Our results are further supported by fluorescence readout from pore arrays and high-speed atomic force microscopy on single pores. This type of dynamic barrier control on the nanoscale provides new possibilities for biomolecular separation and analysis.

Polymer brushes in solid-state nanopores form an impenetrable entropic barrier for proteins

Polymer brushes are widely used to prevent the adsorption of proteins, but the mechanisms by which they operate have remained heavily debated for many decades. We show conclusive evidence that a polymer brush can be a remarkably strong kinetic barrier towards proteins by using poly(ethylene glycol) grafted to the sidewalls of pores in 30 nm thin gold films. Despite consisting of about 90% water, the free coils seal apertures up to 100 nm entirely with respect to serum protein translocation, as monitored label-free through the plasmonic activity of the nanopores. The conclusions are further supported by atomic force microscopy and fluorescence microscopy. A theoretical model indicates that the brush undergoes a morphology transition to a sealing state when the ratio between the extension and the radius of curvature is approximately 0.8. The brush-sealed pores represent a new type of ultrathin filter with potential applications in bioanalytical systems.