Transforming Separation Science with Single-Molecule Methods

A practical guide to the discovery of biomolecules with biostimulant activity

The growing demand for sustainable solutions in agriculture, which are critical for crop productivity and food quality in the face of climate change and the need to reduce agrochemical usage, has brought biostimulants into the spotlight as valuable tools for regenerative agriculture. With their diverse biological activities, biostimulants can contribute to crop growth, nutrient use efficiency, and abiotic stress resilience, as well as to the restoration of soil health. Biomolecules include humic substances, protein lysates, phenolics, and carbohydrates have undergone thorough investigation because of their demonstrated biostimulant activities. Here, we review the process of the discovery and development of extract-based biostimulants, and propose a practical step-by-step pipeline that starts with initial identification of biomolecules, followed by extraction and isolation, determination of bioactivity, identification of active compound(s), elucidation of mechanisms, formulation, and assessment of effectiveness. The different steps generate a roadmap that aims to expedite the transfer of interdisciplinary knowledge from laboratory-scale studies to pilot-scale production in practical scenarios that are aligned with the prevailing regulatory frameworks.

Single-Molecule Fluorescence Investigations of Solute Transport Dynamics in Nanostructured Membrane Separation Materials

Many materials used for membrane separations are composed of nanoscale structures such as pores and domains. Such nanostructures often control the solute permeability and selectivity of the separation membranes. Thus, for future development of highly efficient separation membranes, it is important to understand the structural and chemical properties of these nanostructures and also their influences on solute transport dynamics. For the last two decades, single-molecule fluorescence techniques have been used to measure the detailed dynamics of solute molecules diffusing in various nanostructured materials, giving valuable insights into molecular transport mechanisms influenced by nanoscale material heterogeneity. This Perspective discusses recent single-molecule fluorescence studies on solute diffusion in materials relevant to membrane separations, including dense polymer films and nanoporous materials. These studies have revealed the formation and properties of nanostructures and unique transport dynamics of solute molecules manipulated by their confinement and partitioning to the nanostructures, which play key roles in membrane separations. This Perspective will also point out scientific challenges toward a thorough understanding of molecular-level mechanisms in membrane separations.

Spatially Resolving Size Effects on Diffusivity in Nanoporous Extracellular Matrix-like Materials with Fluorescence Correlation Spectroscopy Super-Resolution Optical Fluctuation Imaging

It is well documented that the nanoscale structures within porous microenvironments greatly impact the diffusion dynamics of molecules. However, how the interaction between the environment and molecules influences the diffusion dynamics has not been thoroughly explored. Here, we show that fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) can be used to accurately measure the diffusion dynamics of molecules within varying matrices such as nanopatterned surfaces and porous agarose hydrogels. Our data demonstrate the robustness of fcsSOFI, where it is possible not only to quantify the diffusion speeds of molecules in heterogeneous media but also to recover the matrix structure with resolution on the order of 100 nm. Using dextran molecules of varying sizes, we show that the diffusion coefficient is sensitive to the change in the molecular hydrodynamic radius. fcsSOFI images further reveal that smaller dextran molecules can freely move through the small pores of the hydrogel and report the detailed porous structure and local diffusion heterogeneities not captured by the average diffusion coefficient. Conversely, bigger dextran molecules are confined and unable to freely move through the hydrogel, highlighting only the larger pore structures. These findings establish fcsSOFI as a powerful tool to characterize spatial and diffusion information of diverse macromolecules within biorelevant matrices.

Single-Molecule Imaging in Commercial Stationary Phase Particles Using Highly Inclined and Laminated Optical Sheet Microscopy

We resolve the three-dimensional, nanoscale locations of single-molecule analytes within commercial stationary phase materials using highly inclined and laminated optical sheet (HILO) microscopy. Single-molecule fluorescence microscopy of chromatography can reveal the molecular heterogeneities that lead to peak broadening, but past work has focused on surfaces designed to mimic stationary phases, which have different physical and chemical properties than the three-dimensional materials used in real columns and membranes. To extend single-molecule measurements to commercial stationary phases, we immobilize individual stationary phase particles and modify our microscope for imaging at further depths with HILO, a method which was originally developed to resolve single molecules in cells of comparable size to column packing materials (∼5-10 μm). We describe and characterize how to change the angle of incidence to achieve HILO so that other researchers can easily incorporate this method onto their existing epi- or total internal reflection fluorescence microscopes. We show improvements up to a 32% in signal-to-background ratio and 118% in the number of single molecules detected within stationary phase particles when using HILO compared to epifluorescence. By controlling the objective position relative to the sample, we produce three-dimensional maps of molecule locations throughout entire stationary phase particles at nanoscale lateral and axial resolutions. The number of localized molecules remains constant axially throughout isolated stationary phase particles and between different particles, indicating that heterogeneity in a separation would not be caused by such affinity differences at microscales but instead kinetic differences at nanoscales on identifiable and distinct adsorption sites.

The competing influence of surface roughness, hydrophobicity, and electrostatics on protein dynamics on a self-assembled monolayer

Surface morphology, in addition to hydrophobic and electrostatic effects, can alter how proteins interact with solid surfaces. Understanding the heterogeneous dynamics of protein adsorption on surfaces with varying roughness is experimentally challenging. In this work, we use single-molecule fluorescence microscopy to study the adsorption of α-lactalbumin protein on the glass substrate covered with a self-assembled monolayer (SAM) with varying surface concentrations. Two distinct interaction mechanisms are observed: localized adsorption/desorption and continuous-time random walk (CTRW). We investigate the origin of these two populations by simultaneous single-molecule imaging of substrates with both bare glass and SAM-covered regions. SAM-covered areas of substrates are found to promote CTRW, whereas glass surfaces promote localized motion. Contact angle measurements and atomic force microscopy imaging show that increasing SAM concentration results in both increasing hydrophobicity and surface roughness. These properties lead to two opposing effects: increasing hydrophobicity promotes longer protein flights, but increasing surface roughness suppresses protein dynamics resulting in shorter residence times. Our studies suggest that controlling hydrophobicity and roughness, in addition to electrostatics, as independent parameters could provide a means to tune desirable or undesirable protein interactions with surfaces.

A new metric for relating macroscopic chromatograms to microscopic surface dynamics: the distribution function ratio (DFR)

Heterogeneous stationary phase chemistry causes chromatographic tailing that lowers separation efficiency and complicates optimizing mobile phase conditions. Model-free metrics are attractive for assessing optimal separation conditions due to the low quantity of information required, but often do not reveal underlying mechanisms that cause tailing, for example, heterogeneous retention modes. We report a new metric, which we call the Distribution Function Ratio (DFR), based on a graphical comparison between the chromatogram and Gaussian cumulative distribution functions, achieving correspondence to ground truth surface dynamics with a single chromatogram. Using a Monte Carlo framework, we show that the DFR can predict the prevalence of heterogeneous retention modes with high precision when the relative desorption rate between modes is known, as in during surface dynamics experiments. Ground truth comparisons reveal that the DFR outperforms both the asymmetry factor and skewness by yielding a one-to-one correspondence with heterogeneous retention mode prevalence over a broad range of experimentally realistic values. Perhaps of more value, we illustrate that the DFR, when combined with the asymmetry factor and skewness, can estimate microscopic surface dynamics, providing valuable insights into surface chemistry using existing chromatographic instrumentation. Connecting ensemble results to microscopic quantities through the lens of simulation establishes a new chemistry-driven route to measuring and advancing separations.

Probing Biosensing Interfaces With Single Molecule Localization Microscopy (SMLM)

Far field single molecule localization microscopy (SMLM) has been established as a powerful tool to study biological structures with resolution far below the diffraction limit of conventional light microscopy. In recent years, the applications of SMLM have reached beyond traditional cellular imaging. Nanostructured interfaces are enriched with information that determines their function, playing key roles in applications such as chemical catalysis and biological sensing. SMLM enables detailed study of interfaces at an individual molecular level, allowing measurements of reaction kinetics, and detection of rare events not accessible to ensemble measurements. This paper provides an update to the progress made to the use of SMLM in characterizing nanostructured biointerfaces, focusing on practical aspects, recent advances, and emerging opportunities from an analytical chemistry perspective.

Computationally-efficient spatiotemporal correlation analysis super-resolves anomalous diffusion

Anomalous diffusion dynamics in confined nanoenvironments govern the macroscale properties and interactions of many biophysical and material systems. Currently, it is difficult to quantitatively link the nanoscale structure of porous media to anomalous diffusion within them. Fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) has been shown to extract nanoscale structure and Brownian diffusion dynamics within gels, liquid crystals, and polymers, but has limitations which hinder its wider application to more diverse, biophysically-relevant datasets. Here, we parallelize the least-squares curve fitting step on a GPU improving computation times by up to a factor of 40, implement anomalous diffusion and two-component Brownian diffusion models, and make fcsSOFI more accessible by packaging it in a user-friendly GUI. We apply fcsSOFI to simulations of the protein fibrinogen diffusing in polyacrylamide of varying matrix densities and super-resolve locations where slower, anomalous diffusion occurs within smaller, confined pores. The improvements to fcsSOFI in speed, scope, and usability will allow for the wider adoption of super-resolution correlation analysis to diverse research topics.