FIB-milled plasmonic nanoapertures allow for long trapping times of individual proteins

Photothermophoretic Splitting of Gold Nanoparticles for Plasmonic Nanopores and Nanonets Sensing

Optical processing of single plasmonic nanoparticles reinvents the way of high-density information storage, high-performance sensing, and high-definition displays. However, such laser-fabricated nanoplasmonics with well-defined hot spots remain elusive due to the diffraction limit of light. Here we show Au nanoparticle (NP) decorated nanopores can be facilely generated with photothermal splitting of single Au NPs embedded in a silica matrix. The extremely high local temperature induced by plasmonic heating renders gradients of the temperature and surface tension around the Au NP, which drives the nanoscale thermophoretic and Marangoni flow of molten Au/silica. As a result, a nanopore decorated with fragmented Au NPs is formed in the silica film, which presents much stronger surface-enhanced Raman scattering as compared to a single Au NP due to the emergence of hot spots. This strategy can be used to generate plasmonic nanopores of various sizes in the silicon nitride (SiNx) films, which further transforms into nanonets at ambient conditions via light-induced reconstruction of silicon nitride membrane. These nanonets can serve as a robust platform for single particle trapping and analysis.

Influence of point mutations on PR65 conformational adaptability: Insights from molecular simulations and nanoaperture optical tweezers

PR65 is the HEAT repeat scaffold subunit of the heterotrimeric protein phosphatase 2A (PP2A) and an archetypal tandem repeat protein. Its conformational mechanics plays a crucial role in PP2A function by opening/closing substrate binding/catalysis interface. Using in silico saturation mutagenesis, we identified PR65 "hinge" residues whose substitutions could alter its conformational adaptability and thereby PP2A function, and selected six mutations that were verified to be expressed and soluble. Molecular simulations and nanoaperture optical tweezers revealed consistent results on the specific effects of the mutations on the structure and dynamics of PR65. Two mutants observed in simulations to stabilize extended/open conformations exhibited higher corner frequencies and lower translational scattering in experiments, indicating a shift toward extended conformations, whereas another displayed the opposite features, confirmed by both simulations and experiments. The study highlights the power of single-molecule nanoaperture-based tweezers integrated with in silico approaches for exploring the effect of mutations on protein structure and dynamics.

Thermometric Analysis of Nanoaperture-Trapped Erbium-Containing Nanocrystals

Temperature changes in plasmonic traps can affect biomolecules and quantum emitters; therefore, several works have sought out the capability of measuring the local temperature. Those works used ionic nanopore currents, fluorescence emission variations, and fluorescence-based diffusion tracking to measure the temperature dependence of shaped nanoapertures in metal films. Here, we make use of a stable erbium-containing NaYF4 nanocrystal that gives local temperature dependence while trapped in the nanoaperture hot spot. Ratiometric analysis of the emission at different wavelengths gives local temperature variation. Since the gold film dominates the thermal characteristic, we find that films of thickness 70, 100, and 130 nm give 0.64, 0.37, and 0.25 K/mW temperature change with laser power. Therefore, using thicker films can be effective in reducing the heating when it is not desired.

Self-induced back-action for aperture trapping: Bethe-Rayleigh theory

A dielectric (nano)particle can influence the local electromagnetic field and thereby alter its interaction with that field through the process of self-induced back-action. While this phenomenon is usually considered theoretically as a change in a cavity resonance frequency, such theoretical approaches are not as appropriate when considering systems away from resonance, such as with a subwavelength aperture in a metal film. Here we consider the interaction between an aperture, modelled with Bethe theory as a magnetic dipole, and a Rayleigh particle, modelled as an electric dipole. Using this magnetic dipole - electric dipole interaction, we quantify the self-induced back-action of the particle on the aperture transmission and the optical trapping potential. The model shows quantitative agreement with finite-difference time-domain simulations. This shows that the physics of self-induced back-action for an aperture and a nanoparticle can be understood in terms of dipole-dipole coupling.

Influence of Point Mutations on PR65 Conformational Adaptability: Insights from Nanoaperture Optical Tweezer Experiments and Molecular Simulations

PR65 is the HEAT-repeat scaffold subunit of the heterotrimeric protein phosphatase 2A (PP2A) and an archetypal tandem-repeat protein, forming a spring-like architecture. PR65 conformational mechanics play a crucial role in PP2A function by opening/closing the substrate-binding/catalysis interface. Using in-silico saturation mutagenesis we identified "hinge" residues of PR65, whose substitutions are predicted to restrict its conformational adaptability and thereby disrupt PP2A function. Molecular simulations revealed that a subset of hinge mutations stabilized the extended/open conformation, whereas another had the opposite effect. By trapping in nanoaperture optical tweezer, we characterized PR65 motion and showed that the former mutants exhibited higher corner frequencies and lower translational scattering, indicating a shift towards extended conformations, whereas the latter showed the opposite behavior. Thus, experiments confirm the conformations predicted computationally. The study highlights the utility of nanoaperture-based tweezers for exploring structure and dynamics, and the power of integrating this single-molecule method with in silico approaches.

Fringe Dielectrophoresis Nanoaperture Optical Trapping with Order of Magnitude Speed-Up for Unmodified Proteins

Single molecule analysis of proteins in an aqueous environment without modification (e.g., labels or tethers) elucidates their biophysics and interactions relevant to drug discovery. By combining fringe-field dielectrophoresis with nanoaperture optical tweezers we demonstrate an order of magnitude faster time-to-trap for proteins when the counter electrode is outside of the solution. When the counter electrode is inside the solution (the more common configuration found in the literature), electrophoresis speeds up the trapping of polystyrene nanospheres, but this was not effective for proteins in general. Since time-to-trap is critical for high-thoughput analysis, these findings are a major advancement to the nanoaperture optical trapping technique for protein analysis.

Optical tweezers for drug discovery

The time taken and the cost of producing novel therapeutic drugs presents a significant burden - a typical target-based drug discovery process involves computational screening of drug libraries, compound assays and expensive clinical trials. This review summarises the value of dynamic conformational information obtained by optical tweezers and how this information can target 'undruggable' proteins. Optical tweezers provide insights into the link between biological mechanisms and structural conformations, which can be used in drug discovery. Developing workflows including software and sample preparation will improve throughput, enabling adoption of optical tweezers in biopharma. As a complementary tool, optical tweezers increase the number of drug candidates, improve the understanding of a target's complex structural dynamics and elucidate interactions between compounds and their targets.

Single molecule DNA origami nanoarrays with controlled protein orientation

The nanoscale organization of functional (bio)molecules on solid substrates with nanoscale spatial resolution and single-molecule control-in both position and orientation-is of great interest for the development of next-generation (bio)molecular devices and assays. Herein, we report the fabrication of nanoarrays of individual proteins (and dyes) via the selective organization of DNA origami on nanopatterned surfaces and with controlled protein orientation. Nanoapertures in metal-coated glass substrates were patterned using focused ion beam lithography; 88% of the nanoapertures allowed immobilization of functionalized DNA origami structures. Photobleaching experiments of dye-functionalized DNA nanostructures indicated that 85% of the nanoapertures contain a single origami unit, with only 3% exhibiting double occupancy. Using a reprogrammed genetic code to engineer into a protein new chemistry to allow residue-specific linkage to an addressable ssDNA unit, we assembled orientation-controlled proteins functionalized to DNA origami structures; these were then organized in the arrays and exhibited single molecule traces. This strategy is of general applicability for the investigation of biomolecular events with single-molecule resolution in defined nanoarrays configurations and with orientational control of the (bio)molecule of interest.

Optical manipulation and assembly of micro/nanoscale objects on solid substrates

Many light-based technologies have been developed to manipulate micro/nanoscale objects such as colloidal particles and biological cells for basic research and practical applications. While most approaches such as optical tweezers are best suited for manipulation of objects in fluidic environments, optical manipulation on solid substrates has recently gained research interest for its advantages in constructing, reconfiguring, or powering solid-state devices consisting of colloidal particles as building blocks. Here, we review recent progress in optical technologies that enable versatile manipulation and assembly of micro/nanoscale objects on solid substrates. Diverse technologies based on distinct physical mechanisms, including photophoresis, photochemical isomerization, optothermal phase transition, optothermally induced surface acoustic waves, and optothermal expansion, are discussed. We conclude this review with our perspectives on the opportunities, challenges, and future directions in optical manipulation and assembly on solid substrates.