Measurements of the size and correlations between ions using an electrolytic point contact

High-Resolution and Low-Noise Single-Molecule Sensing with Bio-Inspired Solid-State Nanopores

Solid-state nanopores have been extensively explored as single-molecule sensors, bearing the potential for the sequencing of DNA. Although they offer advantages in terms of high mechanical robustness, tunable geometry, and compatibility with existing semiconductor fabrication techniques in comparison with their biological counterparts, efforts to sequence DNA with these nanopores have been hampered by insufficient spatial resolution and high noise in the measured ionic current signal. Here we show that these limitations can be overcome by the use of solid-state nanopores featuring a thin, narrow constriction as the sensing region, inspired by biological protein nanopores that have achieved notable success in DNA sequencing. Our extensive molecular dynamics simulations show that these bio-inspired nanopores can provide high spatial resolution equivalent to 2D material nanopores and, meanwhile, significantly inhibit noise levels. A theoretical model is also provided to assess the performance of the bio-inspired nanopore, which could guide its design and optimization.

Boric acid templating synthesis of highly-dense yet ultramicroporous carbons for compact capacitive energy storage

Carbon-based supercapacitors have shown great promise for miniaturized electronics and electric vehicles, but are usually limited by their low volumetric performance, which is largely due to the inefficient utilization of carbon pores in charge storage. Herein, we develop a reliable and scalable boric acid templating technique to prepare boron and oxygen co-modified highly-dense yet ultramicroporous carbons (BUMCs). The carbons are featured with high density (up to 1.62 g cm-3), large specific surface area (up to 1050 m2 g-1), narrow pore distribution (0.4-0.6 nm) and exquisite pore surface functionalities (mainly -BC2O, -BCO2, and -COH groups). Consequently, the carbons show exceptionally compact capacitive energy storage. The optimal BUMC-0.5 delivers an outstanding volumetric capacitance of 431 F cm-3 and a high-rate capability in 1 M H2SO4. In particular, an ever-reported high volumetric energy density of 32.6 Wh L-1 can be harvested in an aqueous symmetric supercapacitor. Our results demonstrate that the -BC2O and -BCO2 groups on the ultramicropore walls can facilitate the internal SO42- ion transport, thus leading to an unprecedented high utilization efficiency of ultramicropores for charge storage. This work provides a new paradigm for construction and utilization of dense and ultramicroporous carbons for compact energy storage.

Detection of Biomolecules Using Solid-State Nanopores Fabricated by Controlled Dielectric Breakdown

Nanopore sensor technology is widely used in biomolecular detection due to its advantages of low cost and easy operation. In a variety of nanopore manufacturing methods, controlled dielectric breakdown has the advantages of a simple manufacturing process and low cost under the premise of ensuring detection performance. In this paper, we have made enhancements to the applied pulses in controlled dielectric breakdown and utilized the improved dielectric breakdown technique to fabricate silicon nitride nanopores with diameters of 5 to 15 nm. Our improved fabrication method offers the advantage of precise control over the nanopore diameter (±0.4 nm) and enhances the symmetry of the nanopore. After fabrication, we performed electrical characterization on the nanopores, and the IV characteristics exhibited high linearity. Subsequently, we conducted detection experiments for DNA and protein using the prepared nanopores to assess the detection performance of the nanopores fabricated using our method. In addition, we also give a physical model of molecule translocation through the nanopores to give a reasonable explanation of the data processing results.

Probing electrophysiological activity of amphiphilic Dynorphin A in planar neutral membranes reveals both ion channel-like activity and neuropeptide translocation

Dynorphin A (DynA) is an endogenous neuropeptide that besides acting as a ligand of the κ-opioid receptor, presents some non-opioid pathophysiological properties associated to its ability to induce cell permeability similarly to cell-penetrating peptides (CPPs). Here, we use electrophysiology experiments to show that amphiphilic DynA generates aqueous pores in neutral membranes similar to those reported previously in charged membranes, but we also find other events thermodynamically incompatible with voltage-driven ion channel activity (i.e. non-zero currents with no applied voltage in symmetric salt conditions, reversal potentials that exceed the theoretical limit for a given salt concentration gradient). By comparison with current traces generated by other amphiphilic molecule known to spontaneously cross membranes, we hypothesize that DynA could directly translocate across neutral bilayers, a feature never observed in charged membranes following the same electrophysiological protocol. Our findings suggest that DynA interaction with the cellular membrane is modulated by the lipid charge distribution, enabling either passive ionic transport via membrane remodeling and pore formation or by peptide direct internalization independent of cellular transduction pathways.

The P. aeruginosa effector Tse5 forms membrane pores disrupting the membrane potential of intoxicated bacteria

The type VI secretion system (T6SS) of Pseudomonas aeruginosa injects effector proteins into neighbouring competitors and host cells, providing a fitness advantage that allows this opportunistic nosocomial pathogen to persist and prevail during the onset of infections. However, despite the high clinical relevance of P. aeruginosa, the identity and mode of action of most P. aeruginosa T6SS-dependent effectors remain to be discovered. Here, we report the molecular mechanism of Tse5-CT, the toxic auto-proteolytic product of the P. aeruginosa T6SS exported effector Tse5. Our results demonstrate that Tse5-CT is a pore-forming toxin that can transport ions across the membrane, causing membrane depolarisation and bacterial death. The membrane potential regulates a wide range of essential cellular functions; therefore, membrane depolarisation is an efficient strategy to compete with other microorganisms in polymicrobial environments.

The Pseudomonas aeruginosa Type 6 secretion effector Tse5 forms pores in the cytoplasmic membrane when ectopically produced and hence has a bacteriolytic effect by depolarising the inner membrane potential.

Calling the amino acid sequence of a protein/peptide from the nanospectrum produced by a sub-nanometer diameter pore

The blockade current that develops when a protein translocates across a thin membrane through a sub-nanometer diameter pore informs with extreme sensitivity on the sequence of amino acids that constitute the protein. The current blockade signals measured during the translocation are called a nanospectrum of the protein. Whereas mass spectrometry (MS) is still the dominant technology for protein identification, it suffers limitations. In proteome-wide studies, MS identifies proteins by database search but often fails to provide high protein sequence coverage. It is also not very sensitive requiring about a femtomole for protein identification. Compared with MS, a sub-nanometer diameter pore (i.e. a sub-nanopore) directly reads the amino acids constituting a single protein molecule, but efficient computational tools are still required for processing and interpreting nanospectra. Here, we delineate computational methods for processing sub-nanopore nanospectra and predicting theoretical nanospectra from protein sequences, which are essential for protein identification.

Fabrication of solid-state nanopores

Nanopores are valuable single-molecule sensing tools that have been widely applied to the detection of DNA, RNA, proteins, viruses, glycans, etc. The prominent sensing platform is helping to improve our health-related quality of life and accelerate the rapid realization of precision medicine. Solid-state nanopores have made rapid progress in the past decades due to their flexible size, structure and compatibility with semiconductor fabrication processes. With the development of semiconductor fabrication techniques, materials science and surface chemistry, nanopore preparation and modification technologies have made great breakthroughs. To date, various solid-state nanopore materials, processing technologies, and modification methods are available to us. In the review, we outline the recent advances in nanopores fabrication and analyze the virtues and limitations of various membrane materials and nanopores drilling techniques.

Angstrom-scale ion channels towards single-ion selectivity

Artificial ion channels with ion permeability and selectivity comparable to their biological counterparts are highly desired for efficient separation, biosensing, and energy conversion technologies. In the past two decades, both nanoscale and sub-nanoscale ion channels have been successfully fabricated to mimic biological ion channels. Although nanoscale ion channels have achieved intelligent gating and rectification properties, they cannot realize high ion selectivity, especially single-ion selectivity. Artificial angstrom-sized ion channels with narrow pore sizes <1 nm and well-defined pore structures mimicking biological channels have accomplished high ion conductivity and single-ion selectivity. This review comprehensively summarizes the research progress in the rational design and synthesis of artificial subnanometer-sized ion channels with zero-dimensional to three-dimensional pore structures. Then we discuss cation/anion, mono-/di-valent cation, mono-/di-valent anion, and single-ion selectivities of the synthetic ion channels and highlight their potential applications in high-efficiency ion separation, energy conversion, and biological therapeutics. The gaps of single-ion selectivity between artificial and natural channels and the connections between ion selectivity and permeability of synthetic ion channels are covered. Finally, the challenges that need to be addressed in this research field and the perspective of angstrom-scale ion channels are discussed.

Structure and dynamics of nanoconfined water and aqueous solutions

This review is devoted to discussing recent progress on the structure, thermodynamic, reactivity, and dynamics of water and aqueous systems confined within different types of nanopores, synthetic and biological. Currently, this is a branch of water science that has attracted enormous attention of researchers from different fields interested to extend the understanding of the anomalous properties of bulk water to the nanoscopic domain. From a fundamental perspective, the interactions of water and solutes with a confining surface dramatically modify the liquid's structure and, consequently, both its thermodynamical and dynamical behaviors, breaking the validity of the classical thermodynamic and phenomenological description of the transport properties of aqueous systems. Additionally, man-made nanopores and porous materials have emerged as promising solutions to challenging problems such as water purification, biosensing, nanofluidic logic and gating, and energy storage and conversion, while aquaporin, ion channels, and nuclear pore complex nanopores regulate many biological functions such as the conduction of water, the generation of action potentials, and the storage of genetic material. In this work, the more recent experimental and molecular simulations advances in this exciting and rapidly evolving field will be reported and critically discussed.

Two-dimensional materials as solid-state nanopores for chemical sensing

Solid-state nanopores as a versatile alternative to biological nanopores have grown tremendously over the last two decades. They exhibit unique characteristics including mechanical robustness, thermal and chemical stability, easy modifications and so on. Moreover, the pore size of a solid-state nanopore could be accurately controlled from sub-nanometers to hundreds of nanometers based on the experimental requirements, presenting better adaptability than biological nanopores. Two-dimensional (2D) materials with single layer thicknesses and highly ordered structures have great potential as solid-state nanopores. In this perspective, we introduced three kinds of substrate-supported 2D material solid-state nanopores, including graphene, MoS2 and MOF nanosheets, which exhibited big advantages compared to traditional solid-state nanopores and other biological counterparts. Besides, we suggested the fabrication and modulation of 2D material solid-state nanopores. We also discussed the applications of 2D materials as solid-state nanopores for ion transportation, DNA sequencing and biomolecule detection.

Ion transport in electrolytes of dielectric nanodevices

Ion transport in electrolytes with nanoscale confinements is of great importance in many fields such as nanofluidics and electrochemical energy devices. The mobility and conductance for ions are often described by the classical Debye-Hückel-Onsager (DHO) theory but this theory fails for ions near dielectric interfaces. We propose a generalized DHO theory by using the Wentzel-Kramers-Brillouin techniques for the solution of the Onsager-Fuoss equation with variable coefficients. The theory allows to quantitatively measure physical quantities of ion transport in nanodevices and is demonstrated to well explain the abnormal increase or decrease of the ionic mobility tuned via the dielectric mismatch. By numerical calculations, our theory unravels the crucial role of the size of confinements and the ionic concentration on the ion transport, and demonstrates that the dielectric polarization can provide a giant enhancement on the conductance of electrolytes in nanodevices. This mechanism provides a practical guide for related nanoscale technologies with controllable transport properties.

Adaptable and Multifunctional Ion-Conducting Aquaporins

Aquaporins function as water and neutral solute channels, signaling hubs, disease virulence factors, and metabolon components. We consider plant aquaporins that transport ions compared to some animal counterparts. These are candidates for important, as yet unidentified, cation and anion channels in plasma, tonoplast, and symbiotic membranes. For those individual isoforms that transport ions, water, and gases, the permeability spans 12 orders of magnitude. This requires tight regulation of selectivity via protein interactions and posttranslational modifications. A phosphorylation-dependent switch between ion and water permeation in AtPIP2;1 might be explained by coupling between the gates of the four monomer water channels and the central pore of the tetramer. We consider the potential for coupling between ion and water fluxes that could form the basis of an electroosmotic transducer. A grand challenge in understanding the roles of ion transporting aquaporins is their multifunctional modes that are dependent on location, stress, time, and development.

Strong Enhancement of Nanoconfined Water Mobility by a Structure Breaking Salt

For the majority of the water present on earth, the two most important factors influencing its behavior are confinement, in either inorganic or organic matrixes, and the presence of solutes. Here, we investigate the effect of confinement in 3 nm pores on water diffusivity in aqueous solutions with archetypical solutes, a structure making (kosmotrope) NaCl and a structure breaking (chaotrope) KCl, up to 1.0 M in concentration. The water diffusivity in bulk aqueous solutions in such a concentration range is known to decrease very slightly in the presence of NaCl and increase very slightly in the presence of KCl. However, here we observe the water diffusivity in confined H₂O-KCl increases by a factor of 2 compared to the pure water diffusivity in the same confinement. This unusually strong cumulative effect of confinement and a structure breaking additive may have profound implications for the mobility and transport of aqueous species in nature.

Selectivity of ion transport in narrow carbon nanotubes depends on the driving force due to drag or drive nature of their active hydration shells

Molecular dynamics simulations have revealed the important roles of hydration shells of ions transported through ultrathin carbon nanotubes (CNTs). In particular, ions driven by electric fields tend to drag their hydration shells behind them, while for ions transported by pressure, their hydration shells can actively drive them. Given the different binding strengths of hydration shells to ions of different sizes, these active roles of hydration shells affect the relative entry rates and driving speeds of ions in CNTs.

Specific adsorption of trivalent cations in biological nanopores determines conductance dynamics and reverses ionic selectivity

Adsorption processes are central to ionic transport in industrial and biological membrane systems. Multivalent cations modulate the conductive properties of nanofluidic devices through interactions with charged surfaces that depend principally on the ion charge number. Considering that ion channels are specialized valves that demand a sharp specificity in ion discrimination, we investigate the adsorption dynamics of trace amounts of different salts of trivalent cations in biological nanopores. We consider here OmpF from Escherichia coli, an archetypical protein nanopore, to probe the specificity of biological nanopores to multivalent cations. We systematically compare the effect of three trivalent electrolytes on OmpF current-voltage relationships and characterize the degree of rectification induced by each ion. We also analyze the open channel current noise to determine the existence of equilibrium/non-equilibrium mechanisms of ion adsorption and evaluate the extent of charge inversion through selectivity measurements. We show that the interaction of trivalent electrolytes with biological nanopores occurs via ion-specific adsorption yielding differential modulation of ion conduction and selectivity inversion. We also demonstrate the existence of non-equilibrium fluctuations likely related to ion-dependent trapping-detrapping processes. Our study provides fundamental information relevant to different biological and electrochemical systems where transport phenomena involve ion adsorption in charged surfaces under nanoscale confinement.

Single-molecule conformational dynamics of viroporin ion channels regulated by lipid-protein interactions

Classic swine fever is a highly contagious and often fatal viral disease that is caused by the classical swine fever virus (CSFV). Protein p7 of CFSV is a prototype of viroporin, a family of small, highly hydrophobic proteins postulated to modulate virus-host interactions during the processes of virus entry, replication and assembly. It has been shown that CSFV p7 displays substantial ion channel activity when incorporated into membrane systems, but a deep rationalization of the size and dynamics of the induced pores is yet to emerge. Here, we use high-resolution conductance measurements and current fluctuation analysis to demonstrate that CSFV p7 channels are ruled by equilibrium conformational dynamics involving protein-lipid interactions. Atomic force microscopy (AFM) confirms the existence of a variety of pore sizes and their tight regulation by solution pH. We conclude that p7 viroporin forms subnanometric channels involved in virus propagation, but also much larger pores (1-10 nm in diameter) with potentially significant roles in virus pathogenicity. Our findings provide new insights into the sources of noise in protein electrochemistry and demonstrate the existence of slow complex dynamics characteristic of crowded systems like biomembrane surfaces.

Water Bridges in Clay Nanopores: Mechanisms of Formation and Impact on Hydrocarbon Transport

Clays are prevalent in the earth's crust and usually deposited in the presence of water. An unusual finding in clays is that under certain conditions, water molecules can collectively form a bridge across a clay-hosted pore. However, there are relatively few studies focused on the formation mechanism of the water bridge in clay nanopores. In this work, we use molecular dynamics simulations to investigate the formation of the water bridge and its influence on fluid transport in slit-shaped illite nanopores. Two different basal illite surface chemistries are constructed: potassium-hydroxyl (P-H) and hydroxyl-hydroxyl (H-H) structures. Because pore size and water concentration are expected to control the formation of the water bridge, our simulations span a wide range of pore sizes and water concentrations. Generally, positive potassium layers and negative hydroxyl groups in P-H nanopore can induce partial charges which in return produce instant and local electric fields, favoring the formation of the water bridge. In P-H nanopores, the water bridge happens at a relatively low water concentration. However, in H-H nanopores, the water bridge only forms at high water concentrations. Additionally, smaller pore sizes favor the formation of water bridges. However, the presence of an electric field promotes the formation of a water bridge even in larger pore sizes in P-H pores. The results also indicate that in both P-H and H-H nanopores, water adsorption films initially create a smooth surface to promote the hydrocarbon flow. In P-H nanopores, further increases in the water concentration causes a sharp decline in the self-diffusion coefficients of the hydrocarbon and water due to the formation of the water bridge. The presence of electric fields in P-H pores can however weaken the confinement effect of illite and promote the hydrocarbon flow. In contrast, in H-H nanopores, the self-diffusion coefficients decline slowly with the increase of water concentration. This is because no water bridge is formed at low water concentrations in H-H nanopores.

Reverse Translocation of Nucleotides through a Carbon Nanotube

We report molecular dynamics (MD) simulations of the reverse translocation of single nucleotides through a narrow carbon nanotube (CNT), with a diameter of 1.36 nm, immersed in a 1 M KCl electrolyte solution under an applied electric field along the tube axis. We observe ion selectivity by the narrow CNT, which leads to a high flow of K⁺ ions, in contrast to a negligible and opposing current of Cl^- ions. The K⁺ ions, driven by the electric field, force a negatively charged single nucleotide into the narrow CNT where it is trapped by the incoming K⁺ ions and water molecules, and the nucleotide is driven in the same direction as the K⁺ ions. This illustrates a novel mechanism of nucleotide reverse translocation that is controlled by ion selectivity. An increase in the CNT diameter to 2.71 nm or an increase in nucleotide chain length both lead to translocation in the normal direction of the applied field. The reverse translocation rate of single nucleotides is correlated to the ionic current of K⁺ ions in the narrow tube, unlike translocation in the normal direction in the wider tube.

Beyond mass spectrometry, the next step in proteomics

Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.