Nanoscale mechanism of molecular transport through the nuclear pore complex as studied by scanning electrochemical microscopy

Graphene oxide-functionalized molecular beacon for real-time interference-free detection of Ki-67 mRNA in living cells

Molecular beacons (MBs) based on hairpin-shaped oligonucleotides are captivating owing to their capability to enable effective real-time detection of cytosolic mRNA in living cells. However, DNase in the nucleus and lysosome could induce the degradation of oligonucleotides in MBs, leading to the generation of false-positive signals. Herein, a graphene oxide (GO) nanosheet was applied as a nanocarrier for MBs to greatly enhance the anti-interference of the easily designed nanoprobe. Advantageously, the absorption capacity of GO for MBs increased with the decrease in pH values, providing the MB-GO nanoprobe with the ability to detect the expression of cytosolic Ki-67 mRNA without interference from DNase Ⅱ in lysosomes. Moreover, the size of GO nanosheets was considerably higher than that of the nuclear pore complex (NPC), which prevented nanoprobes from transition through the NPCs, thereby avoiding the generation of false-positive signals in the nucleus. Altogether, the present work affords a convenient approach for the successful detection of Ki-67 mRNA expression in the cytosol without interference from DNase Ⅰ/Ⅱ in the nucleus/lysosome, which may be potentially further applied for the detection of other cytosolic RNAs.

Nanoscale Quantitative Imaging of Single Nuclear Pore Complexes by Scanning Electrochemical Microscopy

The nuclear pore complex (NPC) is a proteinaceous nanopore that solely and selectively regulates the molecular transport between the cytoplasm and nucleus of a eukaryotic cell. The ∼50 nm-diameter pore of the NPC perforates the double-membrane nuclear envelope to mediate both passive and facilitated molecular transport, thereby playing paramount biological and biomedical roles. Herein, we visualize single NPCs by scanning electrochemical microscopy (SECM). The high spatial resolution is accomplished by employing ∼25 nm-diameter ion-selective nanopipets to monitor the passive transport of tetrabutylammonium at individual NPCs. SECM images are quantitatively analyzed by employing the finite element method to confirm that this work represents the highest-resolution nanoscale SECM imaging of biological samples. Significantly, we apply the powerful imaging technique to address the long-debated origin of the central plug of the NPC. Nanoscale SECM imaging demonstrates that unplugged NPCs are more permeable to the small probe ion than are plugged NPCs. This result supports the hypothesis that the central plug is not an intrinsic transporter, but is an impermeable macromolecule, e.g., a ribonucleoprotein, trapped in the nanopore. Moreover, this result also supports the transport mechanism where the NPC is divided into the central pathway for RNA export and the peripheral pathway for protein import to efficiently mediate the bidirectional traffic.

Transient theory for scanning electrochemical microscopy of biological membrane transport: uncovering membrane-permeant interactions

Scanning electrochemical microscopy (SECM) has emerged as a powerful method to quantitatively investigate the transport of molecules and ions across various biological membranes as represented by living cells. Advantageously, SECM allows for the in situ and non-destructive imaging and measurement of high membrane permeability under simple steady-state conditions, thereby facilitating quantitative data analysis. The SECM method, however, has not provided any information about the interactions of a transported species, i.e., a permeant, with a membrane through its components, e.g., lipids, channels, and carriers. Herein, we propose theoretically that SECM enables the quantitative investigation of membrane-permeant interactions by employing transient conditions. Specifically, we model the membrane-permeant interactions based on a Langmuir-type isotherm to define the strength and kinetics of the interactions as well as the concentration of interaction sites. Finite element simulation predicts that each of the three parameters uniquely affects the chronoamperometric current response of an SECM tip to a permeant. Significantly, this prediction implies that all three parameters are determinable from an experimental chronoamperometric response of the SECM tip. Complimentarily, the steady-state current response of the SECM tip yields the overall membrane permeability based on the combination of the three parameters. Interestingly, our simulation also reveals the optimum strength of membrane-permeant interactions to maximize the transient flux of the permeant from the membrane to the tip.

Nanoelectrochemistry at liquid/liquid interfaces for analytical, biological, and material applications

Herein, we feature our recent efforts toward the development and application of nanoelectrochemistry at liquid/liquid interfaces, which are also known as interfaces between two immiscible electrolyte solutions (ITIES). Nanopipets, nanopores, and nanoemulsions are developed to create the nanoscale ITIES for the quantitative electrochemical measurement of ion transfer, electron transfer, and molecular transport across the interface. The nanoscale ITIES serves as an electrochemical nanosensor to enable the selective detection of various ions and molecules as well as high-resolution chemical imaging based on scanning electrochemical microscopy. The powerful nanoelectroanalytical methods will be useful for biological and material applications as illustrated by in situ studies of solid-state nanopores, nuclear pore complexes, living bacteria, and advanced nanoemulsions. These studies provide unprecedented insights into the chemical reactivity of important biological and material systems even at the single nanostructure level.

Mechanistic Assessment of Metabolic Interaction between Single Oral Commensal Cells by Scanning Electrochemical Microscopy

The human oral microbiome heavily influences the status of oral and systemic diseases through different microbial compositions and complex signaling between microbes. Recent evidence suggests that investigation of interactions between oral microbes can be utilized to understand how stable communities are maintained and how they may preserve health. Herein, we investigate two highly abundant species in the human supragingival plaque, Streptococcus mitis and Corynebacterium matruchotii, to elucidate their real-time chemical communication in commensal harmony. Specifically, we apply nanoscale scanning electrochemical microscopy (SECM) using a submicropipet-supported interface between two immiscible electrolyte solutions as an SECM probe not only to image the permeability of S. mitis and C. matruchotii membranes to tetraethylammonium (TEA⁺) probe ions but also to real-time visualize the metabolic interaction between two microbes via lactate production/consumption at a single-cell level. The metabolic relationship between two strains is quantitatively assessed by determining (1) the passive permeability of both bacterial membranes of 2.4 × 10^-4 cm/s to the free diffusion of TEA⁺, (2) 0.5 mM of the lactate concentration produced by a single S. mitis strain at a rate of 2.7 × 10^-4 cm/s, and (3) a lactate oxidation rate ≥5.0 × 10⁶ s^-1 by an individual C. matruchotii strain. Significantly, this study, for the first time, describes a mechanism of in situ metabolic interaction between oral commensals at the single-cell level through quantitative analysis, which supports the observed in vivo spatial arrangements of these microbes.

Nanogap-Resolved Adsorption-Coupled Electron Transfer by Scanning Electrochemical Microscopy: Implications for Electrocatalysis

Here, we demonstrate for the first time that the mechanism of adsorption-coupled electron-transfer (ACET) reactions can be identified experimentally. The electron transfer (ET) and specific adsorption of redox-active molecules are coupled in many electrode reactions with practical importance and fundamental interest. ACET reactions are often represented by a concerted mechanism. In reductive adsorption, an oxidant is simultaneously reduced and adsorbed as a reductant on the electrode surface through the ACET step. Alternatively, the non-concerted mechanism mediates outer-sphere reduction and adsorption separately when the reductant adsorption is reversible. In electrocatalysis, reversibly adsorbed reductants are ubiquitous and crucial intermediates. Moreover, electrocatalysis is complicated by the mixed mechanism based on simultaneous ACET and outer-sphere ET steps. In this work, we reveal the non-concerted mechanism for ferrocene derivatives adsorbed at highly oriented pyrolytic graphite as simple models. We enable the transient voltammetric mode of nanoscale scanning electrochemical microscopy (SECM) to kinetically control the adsorption step, which is required for the discrimination of non-concerted, concerted, and mixed mechanisms. Experimental voltammograms are compared with each mechanism by employing finite element simulation. The non-concerted mechanism is supported to indicate that the ACET step is intrinsically slower than its outer-sphere counterpart by at least four orders of magnitude. This finding implies that an ACET step is facilitated thermodynamically but may not be necessarily accelerated or catalyzed by the adsorption of the reductant. SECM-based transient voltammetry will become a powerful tool to resolve and understand electrocatalytic ACET reactions at the elementary level.

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.

Exportin-inspired artificial cell nuclear-exporting nanosystems

Inspired by the structural and chemical features of naturally occurring importin/exportin that allows them to pass through the nuclear pore complexes, we successfully developed an artificial nuclear-exporting nanosystem capable of eliminating compounds accumulated abnormally in the nucleus.

Crowding-induced phase separation of nuclear transport receptors in FG nucleoporin assemblies

The rapid (< 1 ms) transport of biological material to and from the cell nucleus is regulated by the nuclear pore complex (NPC). At the core of the NPC is a permeability barrier consisting of intrinsically disordered Phe-Gly (FG) nucleoporins (FG Nups). Various types of nuclear transport receptors (NTRs) facilitate transport by partitioning in the FG Nup assembly, overcoming the barrier by their affinity to the FG Nups, and comprise a significant fraction of proteins in the NPC barrier. In previous work Zahn et al. (2016), we revealed a universal physical behaviour in the experimentally observed binding of two well-characterized NTRs, NTF2 and the larger Importin-β, to different planar assemblies of FG Nups, with the binding behaviour defined by negative cooperativity. This was further validated by a minimal physical model that treated the FG Nups as flexible homopolymers and the NTRs as uniformly cohesive spheres. Here, we build upon our original study by first parametrizing our model to experimental data, and next predicting the effects of crowding by different types of NTRs. We show how varying the amounts of one type of NTR modulates how the other NTR penetrates the FG Nup assembly. Notably, at similar and physiologically relevant NTR concentrations, our model predicts demixed phases of NTF2 and Imp-β within the FG Nup assembly. The functional implication of NTR phase separation is that NPCs may sustain separate transport pathways that are determined by inter-NTR competition.

Physics of the Nuclear Pore Complex: Theory, Modeling and Experiment

The hallmark of eukaryotic cells is the nucleus that contains the genome, enclosed by a physical barrier known as the nuclear envelope (NE). On the one hand, this compartmentalization endows the eukaryotic cells with high regulatory complexity and flexibility. On the other hand, it poses a tremendous logistic and energetic problem of transporting millions of molecules per second across the nuclear envelope, to facilitate their biological function in all compartments of the cell. Therefore, eukaryotes have evolved a molecular "nanomachine" known as the Nuclear Pore Complex (NPC). Embedded in the nuclear envelope, NPCs control and regulate all the bi-directional transport between the cell nucleus and the cytoplasm. NPCs combine high molecular specificity of transport with high throughput and speed, and are highly robust with respect to molecular noise and structural perturbations. Remarkably, the functional mechanisms of NPC transport are highly conserved among eukaryotes, from yeast to humans, despite significant differences in the molecular components among various species. The NPC is the largest macromolecular complex in the cell. Yet, despite its significant complexity, it has become clear that its principles of operation can be largely understood based on fundamental physical concepts, as have emerged from a combination of experimental methods of molecular cell biology, biophysics, nanoscience and theoretical and computational modeling. Indeed, many aspects of NPC function can be recapitulated in artificial mimics with a drastically reduced complexity compared to biological pores. We review the current physical understanding of the NPC architecture and function, with the focus on the critical analysis of experimental studies in cells and artificial NPC mimics through the lens of theoretical and computational models. We also discuss the connections between the emerging concepts of NPC operation and other areas of biophysics and bionanotechnology.

Advanced Materials for Energy-Water Systems: The Central Role of Water/Solid Interfaces in Adsorption, Reactivity, and Transport

The structure, chemistry, and charge of interfaces between materials and aqueous fluids play a central role in determining properties and performance of numerous water systems. Sensors, membranes, sorbents, and heterogeneous catalysts almost uniformly rely on specific interactions between their surfaces and components dissolved or suspended in the water-and often the water molecules themselves-to detect and mitigate contaminants. Deleterious processes in these systems such as fouling, scaling (inorganic deposits), and corrosion are also governed by interfacial phenomena. Despite the importance of these interfaces, much remains to be learned about their multiscale interactions. Developing a deeper understanding of the molecular- and mesoscale phenomena at water/solid interfaces will be essential to driving innovation to address grand challenges in supplying sufficient fit-for-purpose water in the future. In this Review, we examine the current state of knowledge surrounding adsorption, reactivity, and transport in several key classes of water/solid interfaces, drawing on a synergistic combination of theory, simulation, and experiments, and provide an outlook for prioritizing strategic research directions.

Nanoelectrochemical Study of Molecular Transport through the Nuclear Pore Complex

The nuclear pore complex (NPC) is the proteinaceous nanopore that solely mediates the transport of both small molecules and macromolecules between the nucleus and cytoplasm of a eukaryotic cell to regulate gene expression. In this personal account, we introduce recent progress in our nanoelectrochemical study of molecular transport through the NPC. Our work represents the importance of chemistry in understanding and controlling of NPC-mediated molecular transport to enable the efficient and safe delivery of genetic therapeutics into the nucleus, thereby fundamentally contributing to human health. Specifically, we employ nanoscale scanning electrochemical microscopy to test our hypothesis that the nanopore of the NPC is divided by transport barriers concentrically into peripheral and central routes to efficiently mediate the bimodal traffic of protein transport and RNA export, respectively, through cooperative hydrophobic and electrostatic interactions.

Nanoelectrochemistry in the study of single-cell signaling

Label-free biosensing has been the dream of scientists and biotechnologists as reported by Vollmer and Arnold (Nat Methods 5:591-596, 2008). The ability of examining living cells is crucial to cell biology as noted by Fang (Int J Electrochem 2011:460850, 2011). Chemical measurement with electrodes is label-free and has demonstrated capability of studying living cells. In recent years, nanoelectrodes of different functionality have been developed. These nanometer-sized electrodes, coupled with scanning electrochemical microscopy (SECM), have further enabled nanometer spatial resolution study in aqueous environments. Developments in the field of nanoelectrochemistry have allowed measurement of signaling species at single cells, contributing to better understanding of cell biology. Leading studies using nanoelectrochemistry of a variety of cellular signaling molecules, including redox-active neurotransmitter (e.g., dopamine), non-redox-active neurotransmitter (e.g., acetylcholine), reactive oxygen species (ROS), and reactive nitrogen species (RNS), are reviewed here.

Bioinspired Cell Nuclear Nanotransporters Generated by Self-Assembly of Amphiphilic Polysaccharide-Amino Acid Derivatives Conjugates

Development of nanomaterials that surely transport functional biomacromolecules and bioactive synthetic compounds into the cell nucleus must be promising for the generation of nuclear-targeting new technologies. However, the development of nuclear transporting nanomaterials thus still remains a significant challenge, because molecular transport between the cytoplasm and the nucleus of a eukaryotic cell is strictly regulated by the sole gateway through the nuclear envelope, the nuclear pore complexes (NPCs). Here, the rational design of novel artificial nuclear nanotransporters (NucPorters), inspired by importin, naturally occurring nuclear transporters is shown. The NucPorter is generated by simple molecular design: self-assembly of amphiphilic polymers, where a few numbers of hydrophobic amino-acid derivatives with phenyl groups are conjugated to negatively charged hydrophilic heparin. The NucPorter can mimic essential structural and chemical features of importin machinery to pass through the NPCs. Importantly, the NucPorter demonstrates remarkable rapid and high efficient nuclear transport in cultured cells, tissue/organ, and living mice. Moreover, the NucPorter successfully imports both enzymes and synthetic anticancer drugs into the nucleus while maintaining their bioactivity. Thus, the NucPorter provides a promising new route to generate innovative nuclear-targeting medicines, diagnostics, cell imaging and engineering techniques, and drug delivery systems.

Unraveling Mass and Electron Transfer Kinetics at Silica Nanochannel Membrane Modified Electrodes by Scanning Electrochemical Microscopy

An in-depth understanding of kinetic processes convoluting mass and charge transfer at nanoporous membrane modified electrodes is crucial for developing high-performance electrochemical sensors. In this work, we propose a theoretical model to unravel mass (k_m) and electron transfer rate (k_f) from the apparent electrochemical rate constant (k_app) at silica nanoporous membrane (SNM) modified indium tin oxide (ITO) electrodes (designated as SNM/ITO for simplicity). Using scanning electrochemical microscopy (SECM), the k_app of charged redox species was first determined at the SNM/ITO in the absence and presence of surfactant micelles inside SNM. On the basis of the theory, in the presence of micelles inside SNM, k_m equals zero for all charged probes (Ru(NH₃)₆²⁺, Ru(CN)₆^3-, and FcMeOH⁺), thus the SNM behaves as an insulating barrier and the overall electrode reactivity is dominated by the permeability of SNM. After excluding micelles from SNM, the k_m of Ru(CN)₆^3-/4- is strongly dependent on the KCl concentration in the solution, decreasing from 0.23/0.15 mm s^-1 to almost zero upon decreasing the KCl concentration from 1.0 to 0.01 M. In contrast, k_m increases from 1.33 to 2.4 mm s^-1 for Ru(NH₃)₆²⁺ and from 0.18 to 0.33 mm s^-1 for FcMeOH⁺, which are comparable to the electron transfer rate at the underlying ITO electrode surface (0.8 and 0.35 mm s^-1). In these cases, both mass and electron transfer processes are important in determining the overall redox activity of SNM/ITO electrodes. The methodology reported in this work can provide a quantitative way of unraveling these processes and their respective contributions.

Nanoscale electrostatic gating of molecular transport through nuclear pore complexes as probed by scanning electrochemical microscopy

The nuclear pore complex (NPC) is a large protein nanopore that solely mediates molecular transport between the nucleus and cytoplasm of a eukaryotic cell. There is a long-standing consensus that selective transport barriers of the NPC are exclusively based on hydrophobic repeats of phenylalanine and glycine (FG) of nucleoporins. Herein, we reveal experimentally that charged residues of amino acids intermingled between FG repeats can modulate molecular transport through the NPC electrostatically and in a pathway-dependent manner. Specifically, we investigate the NPC of the Xenopus oocyte nucleus to find that excess positive charges of FG-rich nucleoporins slow down passive transport of a polycationic peptide, protamine, without affecting that of a polyanionic pentasaccharide, Arixtra, and small monovalent ions. Protamine transport is slower with a lower concentration of electrolytes in the transport media, where the Debye length becomes comparable to the size of water-filled spaces among the gel-like network of FG repeats. Slow protamine transport is not affected by the binding of a lectin, wheat germ agglutinin, to the peripheral route of the NPC, which is already blocked electrostatically by adjacent nucleoporins that have more cationic residues than anionic residues and even FG dipeptides. The permeability of NPCs to the probe ions is measured by scanning electrochemical microscopy using ion-selective tips based on liquid/liquid microinterfaces and is analysed by effective medium theory to determine the sizes of peripheral and central routes with distinct protamine permeability. Significantly, nanoscale electrostatic gating at the NPC can be relevant not only chemically and biologically, but also biomedically for efficient nuclear import of genetically therapeutic substances.

Nanoscale Intelligent Imaging Based on Real-Time Analysis of Approach Curve by Scanning Electrochemical Microscopy

Scanning electrochemical microscopy (SECM) enables high-resolution imaging by examining the amperometric response of an ultramicroelectrode tip near a substrate. Spatial resolution, however, is compromised for nonflat substrates, where distances from a tip far exceed the tip size to avoid artifacts caused by the tip-substrate contact. Herein, we propose a new imaging mode of SECM based on real-time analysis of the approach curve to actively control nanoscale tip-substrate distances without contact. The power of this software-based method is demonstrated by imaging an insulating substrate with step edges using standard instrumentation without combination of another method for distance measurement, e.g., atomic force microscopy. An ∼500 nm diameter Pt tip approaches down to ∼50 nm from upper and lower terraces of a 500 nm height step edge, which are located by real-time theoretical fitting of an experimental approach curve to ensure the lack of electrochemical reactivity. The tip approach to the step edge can be terminated at <20 nm prior to the tip-substrate contact as soon as the theory deviates from the tip current, which is analyzed numerically afterward to locate the inert edge. The advantageous local adjustment of tip height and tip current at the final point of tip approach distinguishes the proposed imaging mode from other modes based on standard instrumentation. In addition, the glass sheath of the Pt tip is thinned to ∼150 nm to rarely contact the step edge, which is unavoidable and instantaneously detected as an abrupt change in the slope of approach curve to prevent damage of the fragile nanotip.

Single-Entity Electrochemistry of Nanoemulsion: The Nanostructural Effect on Its Electrochemical Behavior

New electrochemical approaches have been applied to investigate nanoemulsions (NEs) for their nanostructures and the relevant electrochemical activity by single-entity electrochemistry (SEE). Herein, we make highly monodisperse NEs with ∼40 nm diameter, composed of biocompatible surfactants, castor oil as plasticizers, and ion exchangers. Dynamic light scattering (DLS) measurements with periodically varying surfactant to oil ratios provide us with a structural implication about uneven distributions of incorporating components inside NEs. To support this structural insight, we apply SEE and selectively monitor electron-transfer reactions occurring at individual NEs containing ferrocene upon each collision onto a Pt ultramicroelectrode. The quantitative analysis of the nanoelectrochemical results along with DLS and transmission electron microscopy (TEM) measurements reveal nanostructured compartments of incorporating components inside NEs and their effect on the electrochemical behavior. Indeed, a tunneling barrier inside NEs could be formed depending on the NE composition, thus determining an electrochemical behavior of NEs, which cannot be differentiated by a general morphological study such as DLS and TEM but by our SEE measurements. Furthermore, by employing the nanopipet voltammetry with an interface between two immiscible electrolyte solutions (ITIES) to mimic the NE interface, we could explicitly investigate that the electron-transfer reaction occurring inside NEs is facilitated by the ion-transfer reaction. Overall, these comprehensive electrochemical approaches enable us to elucidate the relation between structures and the electrochemical functionality of NEs and provide quantitative criteria for the proper compositions of NEs regarding their activity in the electrochemical applications. Also, this finding should be a prerequisite for suitable biomedical/electrochemical applications of NEs.

Probing High Permeability of Nuclear Pore Complexes by Scanning Electrochemical Microscopy: Ca2+ Effects on Transport Barriers

The nuclear pore complex (NPC) solely mediates molecular transport between the nucleus and cytoplasm of a eukaryotic cell to play important biological and biomedical roles. However, it is not well-understood chemically how this biological nanopore selectively and efficiently transports various substances, including small molecules, proteins, and RNAs by using transport barriers that are rich in highly disordered repeats of hydrophobic phenylalanine and glycine intermingled with charged amino acids. Herein, we employ scanning electrochemical microscopy to image and measure the high permeability of NPCs to small redox molecules. The effective medium theory demonstrates that the measured permeability is controlled by diffusional translocation of probe molecules through water-filled nanopores without steric or electrostatic hindrance from hydrophobic or charged regions of transport barriers, respectively. However, the permeability of NPCs is reduced by a low millimolar concentration of Ca2+, which can interact with anionic regions of transport barriers to alter their spatial distributions within the nanopore. We employ atomic force microscopy to confirm that transport barriers of NPCs are dominantly recessed (∼80%) or entangled (∼20%) at the high Ca2+ level in contrast to authentic populations of entangled (∼50%), recessed (∼25%), and "plugged" (∼25%) conformations at a physiological Ca2+ level of submicromolar. We propose a model for synchronized Ca2+ effects on the conformation and permeability of NPCs, where transport barriers are viscosified to lower permeability. Significantly, this result supports a hypothesis that the functional structure of transport barriers is maintained not only by their hydrophobic regions, but also by charged regions.

Polymer translocation through a hairy channel mimicking the inner plug of a nuclear pore complex

A microscopic transport model of a polymer translocating through a nuclear pore complex (NPC) is presented based on self-consistent field theory (SCFT), with the NPC and its nucleoporins mimicked by a hairy channel. Multiple cell environment effects (electrolyte effect, excluded volume effect, NPC drag effect, and hydrophobic effect) are all considered in this hairy channel model. The influence of various parameters (polymer chain length, length of NPC, strength of hydrophobic effect, and excluded volume effect) on translocation time is studied through theoretical analysis and numerical calculation. Numerical simulation results show that an area of low nucleoporin number density exists in the NPC, which facilitates the translocation of the polymer. The results also show that the translocation time curves with increasing NPC length and polymer charge number are concave. In addition, there are critical values for NPC length and polymer charge number for which the translocation time has a minimal value. The translocation time decreases with the increasing strength of the hydrophobic effect and excluded volume effect.

Analysing single live cells by scanning electrochemical microscopy

Scanning electrochemical microscopy (SECM) offers single live cell activities along its topography toward cellular physiology and pathology.

Self-Inhibitory Electron Transfer of the Co(III)/Co(II)-Complex Redox Couple at Pristine Carbon Electrode

Applications of conducting carbon materials for highly efficient electrochemical energy devices require a greater fundamental understanding of heterogeneous electron-transfer (ET) mechanisms. This task, however, is highly challenging experimentally, because an adsorbing carbon surface may easily conceal its intrinsic reactivity through adventitious contamination. Herein, we employ nanoscale scanning electrochemical microscopy (SECM) and cyclic voltammetry to gain new insights into the interplay between heterogeneous ET and adsorption of a Co(III)/Co(II)-complex redox couple at the contamination-free surface of electron-beam-deposited carbon (eC). Specifically, we investigate the redox couple of tris(1,10-phenanthroline)cobalt(II), Co(phen)₃²⁺, as a promising mediator for dye-sensitized solar cells and redox flow batteries. A pristine eC surface overlaid with KCl is prepared in vacuum, protected from contamination in air, and exposed to an ultrapure aqueous solution of Co(phen)₃²⁺ by the dissolution of the protective KCl layer. We employ SECM-based nanogap voltammetry to quantitatively demonstrate that Co(phen)₃²⁺ is adsorbed on the pristine eC surface to electrostatically self-inhibit outer-sphere ET of nonadsorbed Co(phen)₃³⁺ and Co(phen)₃²⁺. Strong electrostatic repulsion among Co(phen)₃²⁺ adsorbates is also demonstrated by SECM-based nanogap voltammetry and cyclic voltammetry. Quantitatively, self-inhibitory ET is characterized by a linear decrease in the standard rate constant of Co(phen)₃²⁺ oxidation with a higher surface concentration of Co(phen)₃²⁺ at the formal potential. This unique relationship is consistent not with the Frumkin model of double layer effects, but with the Amatore model of partially blocked electrodes as extended for self-inhibitory ET. Significantly, the complicated coupling of electron transfer and surface adsorption is resolved by combining nanoscale and macroscale voltammetric methods.

A high spatiotemporal study of somatic exocytosis with scanning electrochemical microscopy and nanoITIES electrodes

Extra-synaptic exocytosis is an essential component of cellular communication. A knowledge gap exists in the exocytosis of the non-redox active transmitter acetylcholine. Using the nano-interface between two immiscible electrolyte solutions and scanning electrochemical microscopy (SECM), a high resolution spatiotemporal study of acetylcholine exocytosis is shown from an individual neuronal soma. The nanoelectrode was positioned ∼140 nm away from the release sites on the soma using an SECM. The quantitative study enables the obtaining of key information related to cellular communication, including extracellular concentration of the neurotransmitter, cellular permeability, Ca2+ dependence on somatic release, vesicle density, number of molecules released and the release dynamics. Measurements were achieved with a high signal to noise ratio of 6-19. The released neurotransmitter with a concentration of 2.7 (±1.0) μM was detected at the nanoelectrodes with radii of 750 nm to 860 nm.

Ultraflat, Pristine, and Robust Carbon Electrode for Fast Electron-Transfer Kinetics

Electron-beam (e-beam) deposition of carbon on a gold substrate yields a very flat (0.43 nm of root-mean-square roughness), amorphous carbon film consisting of a mixture of sp²- and sp³-hybridized carbon with sufficient conductivity to avoid ohmic potential error. E-beam carbon (eC) has attractive properties for conventional electrochemistry, including low background current and sufficient transparency for optical spectroscopy. A layer of KCl deposited by e-beam to the eC surface without breaking vacuum protects the surface from the environment after fabrication until dissolved by an ultrapure electrolyte solution. Nanogap voltammetry using scanning electrochemical microscopy (SECM) permits measurement of heterogeneous standard electron-transfer rate constants (k°) in a clean environment without exposure of the electrode surface to ambient air. The ultraflat eC surface permitted nanogap voltammetry with very thin electrode-to-substrate gaps, thus increasing the diffusion limit for k° measurement to >14 cm/s for a gap of 44 nm. Ferrocene trimethylammonium as the redox mediator exhibited a diffusion-limited k° for the previously KCl-protected eC surface, while k° was 1.45 cm/s for unprotected eC. The k° for Ru(NH₃)₆^3+/2+ increased from 1.7 cm/s for unprotected eC to above the measurable limit of 6.9 cm/s for a KCl-protected eC electrode.

Enhancement of Angiogenesis by Ultrasound-Targeted Microbubble Destruction Combined with Nuclear Localization Signaling Peptides in Canine Myocardial Infarction

Objective

This study aimed to develop a gene delivery system using ultrasound-targeted microbubbles destruction (UTMD) combined with nuclear localization signal (NLS) and investigate its efficacy and safety for therapeutic angiogenesis in canine myocardial infarction (MI) model.

Methods

Fifty MI dogs were randomly divided into 5 groups and transfected with Ang-1 gene plasmid: (i) group A: only injection of microbubbles and Ang-1 plasmid; (ii) group B: only UTMD mediated gene transfection; (iii) group C: UTMD combined with classical NLS mediated gene transfection; (iv) group D: UTMD combined with mutational NLS mediated transfection; and (v) group E: UTMD combined with classical NLS in the presence of a nucleus transport blocker. The mRNA and protein expression of Ang-1 gene, microvessel density (MVD) cardiac troponin I (cTnI), and cardiac function were determined after transfection.

Results

The expression of mRNA and protein of Ang-1 gene in group C was significantly higher than that of the other groups (all P < 0.01). The MVD of group C was 10.2-fold of group A and 8.1-fold of group E (P < 0.01). The cardiac function in group C was significant improvement without cTnI rising.

Conclusions

The gene delivery system composed of UTMD and NLS is efficient and safe.

Protein Transport by the Nuclear Pore Complex: Simple Biophysics of a Complex Biomachine

In eukaryotic cells, transport of molecules between the nucleus and the cytoplasm is facilitated by highly selective and efficient biomachines known as nuclear pore complexes (NPCs). The structural details of NPCs vary across species, with many of their constituent proteins exhibiting relatively low sequence conservation; yet the NPC as a whole retains its general architecture and mechanism of action in all eukaryotes from yeast to humans. This functional conservation in the absence of precise molecular conservation suggests that many aspects of the NPC transport mechanism may be understood based on general biophysical considerations. Accordingly, some aspects of NPC function have been recapitulated in artificial nanochannel mimics, even though they lack certain molecular elements of the endogenous NPC. Herein, we review biophysical aspects of NPC architecture and function and cover recent progress in the field. We also review recent advances in man-made molecular filters inspired by NPCs, and their applications in nanotechnology. We conclude the review with an outlook on outstanding questions in the field and biomedical aspects of NPC transport.

Focused-Ion-Beam-Milled Carbon Nanoelectrodes for Scanning Electrochemical Microscopy

Nanoscale scanning electrochemical microscopy (SECM) has emerged as a powerful electrochemical method that enables the study of interfacial reactions with unprecedentedly high spatial and kinetic resolution. In this work, we develop carbon nanoprobes with high electrochemical reactivity and well-controlled size and geometry based on chemical vapor deposition of carbon in quartz nanopipets. Carbon-filled nanopipets are milled by focused ion beam (FIB) technology to yield a flat disk tip with a thin quartz sheath as confirmed by transmission electron microscopy. The extremely high electroactivity of FIB-milled carbon nanotips is quantified by enormously high standard electron-transfer rate constants of ≥10 cm/s for Ru(NH3)63+. The tip size and geometry are characterized in electrolyte solutions by SECM approach curve measurements not only to determine inner and outer tip radii of down to ~27 and ~38 nm, respectively, but also to ensure the absence of a conductive carbon layer on the outer wall. In addition, FIB-milled carbon nanotips reveal the limited conductivity of ~100 nm-thick gold films under nanoscale mass-transport conditions. Importantly, carbon nanotips must be protected from electrostatic damage to enable reliable and quantitative nanoelectrochemical measurements.

Concentrations dominated membrane permeability variation by fullerol nanoparticles on a single living HeLa cell

The effects in HeLa cell membrane permeability caused by the fullerenols C₆₀(OH)_n with different concentrations were studied by scanning electrochemical microscopy (SECM). We demonstrate that C₆₀(OH)_n has very low cytotoxicity, although it can still have strong effects on the cell membrane permeability. In the presence of 1 × 10^-3 mg mL^-1 (1 ppm) C₆₀(OH)_n, the cell membrane permeability increases by 26% after 76 min, which is reversible. When C₆₀(OH)_n concentration is over 25 × 10^-3 mg mL^-1 (25 ppm), the change in membrane permeability (increased 19%) is irreversible.

Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex

Nuclear Pore Complexes (NPCs) are key cellular transporter that control nucleocytoplasmic transport in eukaryotic cells, but its transport mechanism is still not understood. The centerpiece of NPC transport is the assembly of intrinsically disordered polypeptides, known as FG nucleoporins, lining its passageway. Their conformations and collective dynamics during transport are difficult to assess in vivo. In vitro investigations provide partially conflicting results, lending support to different models of transport, which invoke various conformational transitions of the FG nucleoporins induced by the cargo-carrying transport proteins. We show that the spatial organization of FG nucleoporin assemblies with the transport proteins can be understood within a first principles biophysical model with a minimal number of key physical variables, such as the average protein interaction strengths and spatial densities. These results address some of the outstanding controversies and suggest how molecularly divergent NPCs in different species can perform essentially the same function.

DOI:http://dx.doi.org/10.7554/eLife.10785.001

Animal, plant and fungal cells contain a structure called the nucleus, inside which the genetic material of the cell is stored. For the cell to work properly, certain proteins and other molecules need to be able to enter and exit the nucleus. This transport is carried out by pore-like molecular “devices” known as Nuclear Pore Complexes, whose architecture and mode of operation are unique among cellular transporters.

Nuclear Pore Complexes are charged with a daunting task of deciding which of the hundreds of molecules it conducts per second should go through and which should not. Small molecules can pass freely through Nuclear Pore Complexes. However, larger molecules can only pass through the pore efficiently if they are bound to specialized transport proteins that interact with the proteins – called FG nucleoporins – that line the pore. A unique feature of the FG nucleoporins is that, unlike typical proteins, they do not have a defined three-dimensional structure. Instead, they form a soft and pliable lining inside the Nuclear Pore Complex passageway.

Exactly how interacting with transport proteins affects the structure and spatial arrangements of the FG nucleoporins in a way that allows them to control transport is not well understood. This is in part because existing experimental techniques are unable to study the structures of the FG nucleoporins in enough detail to track how they change during transport. The complexity and the diversity of the FG nucleoporins also make them difficult to model in detail.

Vovk, Gu et al. have developed a theoretical model that is based on just three basic physical properties of the FG nucleoporins – their flexibility, their ability to interact with each other, and their binding with the transport proteins. Future work can refine the model by incorporating further molecular details about the interactions between FG nucleoporins and transport proteins.

The predictions made by this simple model agree well with experimental results in a wide range of situations – from single molecules to complex spatial assemblies. They also explain why some of the experimental results appear to contradict each other and suggest how several outstanding controversies in the field can be reconciled. Because the model invokes only fundamental physical principles of FG nucleoporin assemblies, it shows that some of their general properties do not depend on the exact conditions. In particular, this might shed light on why Nuclear Pore Complexes in different organisms perform essentially the same function, although the details of their molecular structure may differ. This also suggests how the FG nucleoporins can be manipulated to build artificial devices based on the same principles.

DOI:http://dx.doi.org/10.7554/eLife.10785.002

Electrochemical Detection of Single Phospholipid Vesicle Collisions at a Pt Ultramicroelectrode

We report the collision behavior of single unilamellar vesicles, composed of a bilayer lipid membrane (BLM), on a platinum (Pt) ultramicroelectrode (UME) by two electrochemical detection methods. In the first method, the blocking of a solution redox reaction, induced by the single vesicle adsorption on the Pt UME, can be observed in the amperometric i-t response as current steps during the electrochemical oxidation of ferrocyanide. In the second technique, the ferrocyanide redox probe is directly encapsulated inside vesicles and can be oxidized during the vesicle collision on the UME if the potential is poised positive enough for ferrocyanide oxidation to occur. In the amperometric i-t response for the latter experiment, a current spike is observed. Here, we report the vesicle blocking (VB) method as a relevant technique for determining the vesicle solution concentration from the collisional frequency and also for observing the vesicle adhesion on the Pt surface. In addition, vesicle reactor (VR) experiments show clear evidence that the lipid bilayer membrane does not collapse or break open at the Pt UME during the vesicle collision. Because the bilayer is too thick for electron tunneling to occur readily, an appropriate concentration of a surfactant, such as Triton X-100 (TX100), was added in the VR solution to induce loosening of the bilayer (transfection conditions), allowing the electrode to oxidize the contents of the vesicle. With this technique, the TX100 effect on the vesicle lipid bilayer permeability can be evaluated through the current spike charge and frequency corresponding to redox vesicle collisions.

Multiscale electrochemistry of hydrogels embedding conductive nanotubes

The local functionalities of biocompatible objects can be characterized under conditions similar to the operating ones, using scanning electrochemical microscopy (SECM). In the case of alginate beads entrapping carbon nanotubes (CNTs), SECM allows evidencing of the local conductivity, organization, and communication between the CNTs. It shows that the CNT network is active enough to allow long range charge evacuation, enabling the use of alginate/CNT beads as soft 3D electrodes. Direct connection or local interrogation by a microelectrode allows visualization of their communication as a network and eventually the study of them individually at the nanoscale.

Study of the ion-channel behavior on glassy carbon electrode supported bilayer lipid membranes stimulated by perchlorate anion

In this paper, a kind of didodecyldimethylammonium bromide (DDAB) layer membranes was supported on a glassy carbon electrode (GCE). We studied the ion channel behavior of the supported bilayer lipid membrane by scanning electrochemical microscopy (SCEM) in tris(2,2'-bipyridine) ruthenium(II) solution. Perchlorate anion was used as a presence of stimulus and ruthenium(II) complex cations as the probing ions for the measurement of SECM, the lipid membrane channel was opened and exhibited the behavior of distinct SECM positive feedback curve. The channel was in a closed state in the absence of perchlorate anions while reflected the behavior of SECM negative feedback curve. The rates of electron transfer reaction in the lipid membranes surface were detected and it was dependant on the potential of SECM.

Probing the disordered domain of the nuclear pore complex through coarse-grained molecular dynamics simulations

The distribution of disordered proteins (FG-nups) that line the transport channel of the nuclear pore complex (NPC) is investigated by means of coarse-grained molecular dynamics simulations. A one-bead-per-amino-acid model is presented that accounts for the hydrophobic/hydrophilic and electrostatic interactions between different amino acids, polarity of the solvent, and screening of free ions. The results indicate that the interaction of the FG-nups forms a high-density, doughnut-like distribution inside the NPC, which is rich in FG-repeats. We show that the obtained distribution is encoded in the amino-acid sequence of the FG-nups and is driven by both electrostatic and hydrophobic interactions. To explore the relation between structure and function, we have systematically removed different combinations of FG-nups from the pore to simulate inviable and viable NPCs that were previously studied experimentally. The obtained density distributions show that the maximum density of the FG-nups inside the pore does not exceed 185 mg/mL in the inviable NPCs, whereas for the wild-type and viable NPCs, this value increases to 300 mg/mL. Interestingly, this maximum density is not correlated to the total mass of the FG-nups, but depends sensitively on the specific combination of essential Nups located in the central plane of the NPC.