Precision platform for convex lens-induced confinement microscopy

Dynamics of polymer chains confined to a periodic cylinder: molecular dynamics simulation vs. Lifson-Jackson formula

The dynamics of polymer chains confined to a periodic cylinder is explored using molecular dynamics simulation and theoretical analysis. The cylinder is divided into two cavities in one periodicity: one cavity consists of a channel of length L1 and diameter D1 and another cavity is a channel of length L2 and diameter D2. For L1 = L2 = L/2, the diffusion coefficient D of a single confined polymer chain decreases rapidly with increase in periodicities L. For a fixed periodicity with L = L1 + L2 = constant, the diffusion coefficient D of a single confined polymer chain shows strong dependence on L1 (or L2). Moreover, for a multi-chain system with L1 = L2, the diffusion coefficient D shows strong non-monotonic dependence on the chain monomer density ρ, and the confined polymer chains diffuse fastest for ρ = 0.068, in which there are three polymer chains in two periodicities as well as two opposing effects: one is that the excluded volume effect between polymer chains can reduce the free energy barrier, and another is that when the chain monomer density ρ increases further, the entanglement effect increases, which leads to that the diffusion coefficient D decreases as ρ increases. Finally, we found that the diffusion coefficient D has a similar oscillation relationship with the ratio of R/L for different chain lengths N and different periodicity L, and the oscillation amplitude decreases gradually as R/L increases; here R is the mean end-to-end distance of a single confined polymer chain, i.e., . From the view of free energy potential, both the width of the free energy potential well and the height of the free energy potential barrier govern simultaneously the diffusion behavior of confined polymer chains. According to the mean force potential (PMF) based on the weighted histogram analysis method (WHAM), we found that our results agree very well with the theoretical analysis using the Lifson-Jackson formula. Our investigation may help us understand the dynamics of particles in a periodic medium, which is one of the interesting problems in many different fields of science, such as physics, chemistry and biology.

Effects of Molecular Weight and Surface Interactions on Polymer Diffusion in Confinement

Understanding the transport and thermodynamics of polymers in confined spaces is helpful for many separation processes like water purification, drug delivery, and oil recovery. Specifically, for water purification, dextran has been used as a "model" foulant. Uncovering how these polymers interact in confinement can reduce the fouling of organic membranes and will lead to better separation processes overall. We have determined the diffusion coefficient, D, of dextran and sodium polyacrylate in convex lens-induced confinement using differential dynamic microscopy. In this setup, the gap height ranges continuously from 0.077-21.8 μm. It was found that polymer diffusion becomes slower in higher confinement, which is consistent with a change in the increase of the hydrodynamic resistance to macromolecule motion and depends on the surface properties. These findings indicate that dextran diffusion changes in confinement and can lead to a better understanding of separation processes.

Biophysical Reviews ‘Meet the Editors Series’ — a profile of Sabrina Leslie

It is my pleasure to introduce myself to the readers of Biophysical Reviews as part of the ‘Meet the Editors Series’.

Diffusive dynamics of charged nanoparticles in convex lens-induced confinement

Transport through heterogeneous confined geometries is encountered in many processes and applications such as filtration, drug delivery, and enhanced oil recovery. We have used differential dynamic microscopy (DDM) and particle tracking to investigate dynamics of 36 nm negatively-charged polystyrene particles in convex lens-induced confinement (CLiC). The confinement gap height was controlled from 0.085 μm to 3.6 mm by sandwiching the aqueous particle solution between a glass coverslip and a convex lens using a homemade sample holder. With an inverted fluorescence microscope, sequences of micrographs were taken at various radial positions and gap heights for five particle concentrations (i.e. φ = 0.5 × 10^-5, 1 × 10^-5, 5 × 10^-5, 10 × 10^-5, 50 × 10^-5) and ionic strengths ranging from 10^-3 to 150 mM. The resulting image structure functions were fitted with a simple exponential model to extract the ensemble-averaged diffusive dynamics. It was found that particle diffusion was more hindered as a function of increased confinement. In addition, the ensemble-averaged diffusion coefficient was found to depend on the bulk concentration, and the concentration dependence increased as a function of confinement. Increasing particle and salt concentration led to confinement-dependent adsorption onto the geometry surface. Overall, we show that CLiC devices are simple and effective and can be used to study dynamics in continuous confinement from sub 100 nm to 100's of μm. These findings could lead to better understanding of separations and interactions in confining devices.

Simultaneous, Single-Particle Measurements of Size and Loading Give Insights into the Structure of Drug-Delivery Nanoparticles

Nanoparticles are a promising solution for delivery of a wide range of medicines and vaccines. Optimizing their design depends on being able to resolve, understand, and predict biophysical and therapeutic properties, as a function of design parameters. While existing tools have made great progress, gaps in understanding remain because of the inability to make detailed measurements of multiple correlated properties. Typically, an average measurement is made across a heterogeneous population, obscuring potentially important information. In this work, we develop and apply a method for characterizing nanoparticles with single-particle resolution. We use convex lens-induced confinement (CLiC) microscopy to isolate and quantify the diffusive trajectories and fluorescent intensities of individual nanoparticles trapped in microwells for long times. First, we benchmark detailed measurements of fluorescent polystyrene nanoparticles against prior data to validate our approach. Second, we apply our method to investigate the size and loading properties of lipid nanoparticle (LNP) vehicles containing silencing RNA (siRNA), as a function of lipid formulation, solution pH, and drug-loading. By taking a comprehensive look at the correlation between the intensity and size measurements, we gain insights into LNP structure and how the siRNA is distributed in the LNP. Beyond introducing an analytic for size and loading, this work allows for future studies of dynamics with single-particle resolution, such as LNP fusion and drug-release kinetics. The prime contribution of this work is to better understand the connections between microscopic and macroscopic properties of drug-delivery vehicles, enabling and accelerating their discovery and development.

Diffusion of Short Semiflexible DNA Polymer Chains in Strong and Moderate Confinement

In many technological applications, DNA is confined within nanoenvironments that are smaller than the size of the unconfined polymer in solution. However, the dependence of the diffusion coefficient on molecular weight and characteristic confinement dimension remains poorly understood in this regime. Here, convex lens-induced confinement (CLiC) was leveraged to examine how the diffusion of short DNA fragments varied as a function of slit height by using single-molecule fluorescence tracking microscopy. The diffusion coefficient followed approximate power law behavior versus confinement height, with exponents of 0.27 ± 0.01, 0.32 ± 0.02, and 0.42 ± 0.06 for 692, 1343, and 2686 base pair chains, respectively. The weak dependence on slit height suggests that shorter semiflexible chains may adopt increasingly rodlike conformations and therefore experience weaker excluded-volume interactions as the confinement dimension is reduced. The diffusion coefficient versus molecular weight also exhibited apparent power law behavior, with exponents that varied slightly (from -0.89 to -0.85) with slit height, consistent with hydrodynamic interactions intermediate between Rouse and Zimm model predictions.

A Method to Quantify Molecular Diffusion within Thin Solvated Polymer Films: A Case Study on Films of Natively Unfolded Nucleoporins

We present a method to probe molecular and nanoparticle diffusion within thin, solvated polymer coatings. The device exploits the confinement with well-defined geometry that forms at the interface between a planar and a hemispherical surface (of which at least one is coated with polymers) in close contact and uses this confinement to analyze diffusion processes without interference of exchange with and diffusion in the bulk solution. With this method, which we call plane-sphere confinement microscopy (PSCM), information regarding the partitioning of molecules between the polymer coating and the bulk liquid is also obtained. Thanks to the shape of the confined geometry, diffusion and partitioning can be mapped as a function of compression and concentration of the coating in a single experiment. The method is versatile and can be integrated with conventional optical microscopes; thus it should find widespread use in the many application areas exploiting functional polymer coatings. We demonstrate the use of PSCM using brushes of natively unfolded nucleoporin domains rich in phenylalanine-glycine repeats (FG domains). A meshwork of FG domains is known to be responsible for the selective transport of nuclear transport receptors (NTRs) and their macromolecular cargos across the nuclear envelope that separates the cytosol and the nucleus of living cells. We find that the selectivity of NTR uptake by FG domain films depends sensitively on FG domain concentration and that the interaction of NTRs with FG domains obstructs NTR movement only moderately. These observations contribute important information to better understand the mechanisms of selective NTR transport.

Single-cell analysis for drug development using convex lens-induced confinement imaging

New technologies have powered rapid advances in cellular imaging, genomics and phenotypic analysis in life sciences. However, most of these methods operate at sample population levels and provide statistical averages of aggregated data that fail to capture single-cell heterogeneity, complicating drug discovery and development. Here we demonstrate a new single-cell approach based on convex lens-induced confinement (CLiC) microscopy. We validated CLiC on yeast cells, demonstrating subcellular localization with an enhanced signal-to-noise and fluorescent signal detection sensitivity compared with traditional imaging. In the live-cell CLiC assay, cellular proliferation times were consistent with flask culture. Using methotrexate, we provide drug response data showing a fivefold cell size increase following drug exposure. Taken together, CLiC enables high-quality imaging of single-cell drug response and proliferation for extended observation periods.

Standalone interferometry-based calibration of convex lens-induced confinement microscopy with nanoscale accuracy

Strongly confined environments (confined dimensions between 1-100 nm) represent unique challenges and opportunities for understanding and manipulating molecular behavior due to the significant effects of electric double layers, high surface-area to volume ratios, and other phenomena at the nanoscale. Convex Lens-induced Confinement (CLiC) can be used to analyze the dynamics of individual molecules or particles confined in a planar slit geometry with continuously varying gap thickness. We describe an interferometry-based method for precise measurement of the slit pore geometry. Specifically, this approach permitted accurate characterization of separation distances as small as 5 nm, with 1 nm precision, without a priori knowledge or assumptions about the contact geometry, as well as a greatly simplified experimental setup that required only a lens, coverslip, and inverted microscope. The interferometry-based measurement of gap height offered a distinct advantage over conventional fluorescent dye-based methods; e.g., accurate interferometric height measurements were made at low gap heights regardless of solution conditions, while the concentration of fluorescent dye was significantly impacted by solution conditions such as ionic strength or pH. The accuracy of the interferometric measurements was demonstrated by comparing the experimentally measured concentration of a charged fluorescent dye as a function of gap thickness with dye concentration profiles calculated using Debye-Hückel theory. Accurate characterization of nanoscale gap thickness will enable researchers to study a variety of practical and biologically relevant systems within the CLiC geometry.

Miniaturized flow cell with pneumatically-actuated vertical nanoconfinement for single-molecule imaging and manipulation

Convex Lens-induced Confinement (CLiC) is a single-molecule imaging technique that uses a deformable glass flow cell to gently trap, manipulate, and visualize single molecules within micro- and nano-structures, to enable a wide range of applications. Here, we miniaturize the CLiC flow cell, from 25 × 25 to 3 × 3 mm 2 and introduce pneumatic control of the confinement. Miniaturization of the flow cell improves fabrication throughput by almost two orders of magnitude and, advantageous for pharmaceutical and diagnostic applications where samples are precious, significantly lowers the internal volume from microliters to nanoliters. Pneumatic control of the device reduces the confinement gradient and improves mechanical stability while maintaining low autofluorescence and refractive index-matching with oil-immersion objectives. To demonstrate our "mini CLiC" system, we confine and image DNA in sub-50 nm nanogrooves, with high DNA extension consistent with the Odijk confinement regime.

Transverse dielectrophoretic-based DNA nanoscale confinement

Confinement of single molecules within nanoscale environments is crucial in a range of fields, including biomedicine, genomics, and biophysics. Here, we present a method that can concentrate, confine, and linearly stretch DNA molecules within a single optical field of view using dielectrophoretic (DEP) force. The method can convert an open surface into one confining DNA molecules without a requirement for bonding, hydrodynamic or mechanical components. We use a transverse DEP field between a top coverslip and a bottom substrate, both of which are coated with a transparent conductive material. Both layers are attached using double-sided tape, defining the chamber. The nanofeatures lie at the “floor” and do not require any bonding. With the application of an alternating (AC) electric field (2 V_p-p) between the top and bottom electrodes, a DEP field gradient is established and used to concentrate, confine and linearly extend DNA in nanogrooves as small as 100-nm in width. We also demonstrate reversible loading/unloading of DNA molecules into nanogrooves and nanopits by switching frequency (between 10 kHz to 100 kHz). The technology presented in this paper provides a new method for single-molecule trapping and analysis.

Subnanometer structure and function from ion beams through complex fluidics to fluorescent particles

The vertical dimensions of complex nanostructures determine the functions of diverse nanotechnologies. In this paper, we investigate the unknown limits of such structure-function relationships at subnanometer scales. We begin with a quantitative evaluation of measurement uncertainty from atomic force microscopy, which propagates through our investigation from ion beam fabrication to fluorescent particle characterization. We use a focused beam of gallium ions to subtractively pattern silicon surfaces, and silicon nitride and silicon dioxide films. Our study of material responses quantifies the atomic limits of forming complex topographies with subnanometer resolution of vertical features over a wide range of vertical and lateral dimensions. Our results demonstrate the underutilized capability of this standard system for rapid prototyping of subnanometer structures in hard materials. We directly apply this unprecedented dimensional control to fabricate nanofluidic devices for the analytical separation of colloidal nanoparticles by size exclusion. Optical microscopy of single nanoparticles within such reference materials establishes a subnanometer limit of the fluidic manipulation of particulate matter and enables critical-dimension particle tracking with subnanometer accuracy. After calibrating for optical interference within our multifunctional devices, which also enables device metrology and integrated spectroscopy, we reveal an unexpected relationship between nanoparticle size and emission intensity for common fluorescent probes. Emission intensity increases supervolumetrically with nanoparticle diameter and then decreases as nanoparticles with different diameters photobleach to similar values of terminal intensity. We propose a simple model to empirically interpret these surprising results. Our investigation enables new control and study of structure-function relationships at subnanometer scales.

Parallelized cytoindentation using convex micropatterned surfaces

Here we present a high-throughput, parallelized cytoindentor for local compression of live cells. The cytoindentor uses convex lens-induced confinement (CLiC) to indent micrometer-sized areas in single cells and/or populations of cells with submicron precision. This is accomplished using micropatterned poly(dimethylsiloxane) (PDMS) films that are adhered to a convex lens to create arrays of extrusions referred to here as "posts." These posts caused local deformation of subcellular regions without any evidence of cell lysis upon CLiC indentation. Our micropost arrays were also functionalized with glycoproteins, such as fibronectin, to both pull and compress cells under customized confinement geometries. Measurements of Chinese hamster ovary (CHO-K1) cell migration trajectories and oxidative stress showed that the CLiC device did not damage or significantly stress the cells. Our novel tool opens a new area of investigation for visualizing mechanobiology and mechanochemistry within living cells, and the high-throughput nature of the technique will streamline investigations as current tools for mechanically probing material properties and molecular dynamics within cells, such as traditional cytoindentors and atomic force microscopy (AFM), are typically restricted to single-cell manipulation.

Single-Particle Tracking of Human Lipoproteins

Lipoproteins, such as high-density lipoprotein (HDL), low-density lipoprotein (LDL), and very-low density lipoprotein (VLDL), play a critical role in heart disease. Lipoproteins vary in size and shape as well as in their apolipoprotein content. Here, we developed a new experimental framework to study freely diffusing lipoproteins from human blood, allowing analysis of even the smallest HDL with a radius of 5 nm. In an easily constructed confinement chamber, individual HDL, LDL, and VLDL particles labeled with three distinct fluorophores were simultaneously tracked by wide-field fluorescence microscopy and their sizes were determined by their motion. This technique enables studies of individual lipoproteins in solution and allows characterization of the heterogeneous properties of lipoproteins which affect their biological function but are difficult to discern in bulk studies.

Development of a platform for single cell genomics using convex lens-induced confinement

We demonstrate a lab-on-a-chip that combines micro/nano-fabricated features with a Convex Lens-Induced Confinement (CLIC) device for the in situ analysis of single cells. A complete cycle of single cell analysis was achieved that includes: cell trapping, cell isolation, lysis, protein digestion, genomic DNA extraction and on-chip genomic DNA linearization. The ability to dynamically alter the flow-cell dimensions using the CLIC method was coupled with a flow-control mechanism for achieving efficient cell trapping, buffer exchange, and loading of long DNA molecules into nanofluidic arrays. Finite element simulation of fluid flow gives rise to optimized design parameters for overcoming the high hydraulic resistance present in the micro/nano-confinement region. By tuning design parameters such as the pressure gradient and CLIC confinement, an efficient on-chip single cell analysis protocol can be obtained. We demonstrate that we can extract Mbp long genomic DNA molecules from a single human lybphoblastoid cell and stretch these molecules in the nanochannels for optical interrogation.

Open-frame system for single-molecule microscopy

We present the design and construction of a versatile, open frame inverted microscope system for wide-field fluorescence and single molecule imaging. The microscope chassis and modular design allow for customization, expansion, and experimental flexibility. We present two components which are included with the microscope which extend its basic capabilities and together create a powerful microscopy system: A Convex Lens-induced Confinement device provides the system with single-molecule imaging capabilities, and a two-color imaging system provides the option of imaging multiple molecular species simultaneously. The flexibility of the open-framed chassis combined with accessible single-molecule, multi-species imaging technology supports a wide range of new measurements in the health, nanotechnology, and materials science research sectors.

Convex lens-induced nanoscale templating

We demonstrate a new platform, convex lens-induced nanoscale templating (CLINT), for dynamic manipulation and trapping of single DNA molecules. In the CLINT technique, the curved surface of a convex lens is used to deform a flexible coverslip above a substrate containing embedded nanotopography, creating a nanoscale gap that can be adjusted during an experiment to confine molecules within the embedded nanostructures. Critically, CLINT has the capability of transforming a macroscale flow cell into a nanofluidic device without the need for permanent direct bonding, thus simplifying sample loading, providing greater accessibility of the surface for functionalization, and enabling dynamic manipulation of confinement during device operation. Moreover, as DNA molecules present in the gap are driven into the embedded topography from above, CLINT eliminates the need for the high pressures or electric fields required to load DNA into direct-bonded nanofluidic devices. To demonstrate the versatility of CLINT, we confine DNA to nanogroove and nanopit structures, demonstrating DNA nanochannel-based stretching, denaturation mapping, and partitioning/trapping of single molecules in multiple embedded cavities. In particular, using ionic strengths that are in line with typical biological buffers, we have successfully extended DNA in sub-30-nm nanochannels, achieving high stretching (90%) that is in good agreement with Odijk deflection theory, and we have mapped genomic features using denaturation analysis.