Solid-State Nanopores for Biomolecular Analysis and Detection

Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.

Sodium current preserves electrical excitability in the heart of hibernating ground squirrel (Citellus undulatus)

Hibernating mammals are capable of maintaining normal cardiac function at low temperatures. Excitability of cardiac myocytes crucially depends on the fast sodium current (I_Na), which is decreased in hypothermia due to both depolarization of resting membrane potential and direct negative effect of low temperature. Therefore, I_Na in hibernating mammals should have specific features allowing to maintain excitability of myocardium at low temperatures. The current-voltage dependence of I_Na, its steady-state inactivation and activation and recovery from inactivation were studied in winter hibernating (WH) and summer active (SA) ground squirrels and in rats using whole-cell patch clamp at 10 °C and 20 °C. I_Na peak amplitude and the parameters of steady-state activation and inactivation curves did not differ between SA and WH ground squirrels at both temperatures. However, at both temperatures strong positive shift of activation and inactivation curves by 5-12 mV was observed in both WH and SA ground squirrels if compared to rats. This peculiarity of cardiac I_Na in ground squirrels helps to maintain excitability in conditions of depolarized resting membrane potential. The time course of I_Na recovery from inactivation at 10 °C was faster in WH than in SA ground squirrels, which could ensure normal activation of myocardium during hibernation.

All-Atom Molecular Dynamics Simulations of Membrane-Spanning DNA Origami Nanopores

Building on the recent technological advances, all-atom molecular dynamics (MD) simulations have become an indispensable tool to study the molecular behavior at nanoscale. Molecular simulations have been used to characterize the structure, dynamics, and mechanical and electrical properties of DNA origami objects. In this chapter we describe a method to build all-atom model of lipid-spanning DNA origami nanopores and perform molecular dynamics simulations in explicit electrolyte solutions.

Environmental noise reduction for tunable resistive pulse sensing of extracellular vesicles

Extracellular vesicles (EVs) bearing biomolecules from parental cells can represent a novel source of disease biomarkers and are under intensive study for their clinical potential. Tunable resistive pulse sensing (TRPS) quantifies the magnitude of a small ionic resistive pulse current to determine the size, concentration, and zeta potential of EVs. Environmental noise is a common limiting factor that affects the precision of sensing devices. TRPS is particularly vulnerable to environmental noise, including both mechanical and electrical. The upper detection limit of the TRPS relies on the physical size of the elastomeric tunable nanopore. The lower limit relies on the electrical signal-to-noise ratio. Guided by simulation, we designed an external device to suppress environmental noise for TRPS measurement. Both mechanical and electrical environmental noise reductions were observed after using the shield. The study also validated the noise reduction function of the shield by quantifying EVs from different cell origins. Detection of EVs smaller than 200 nm was improved by using the shield; which was reported challenging for conventional quantification methods. The study highlighted a feasible approach to solve environmental noise challenges for TRPS based EV quantification.

A theoretical understanding of ionic current through a nanochannel driven by a viscosity gradient

HYPOTHESIS

Different thermodynamic forces owing to the gradient of temperature, electrical potential, or concentration can drive ionic current through charged membranes. It has been recently shown that a viscosity gradient can drive an electrical current through a negatively charged nanochannel (Wiener and Stein, arXiv: 1807.09106). A model description of this phenomenon, based on the Maxwell-Stefan equation will help unravel the dominating physical mechanisms in so-called visco-migration.

THEORY

To understand the physical mechanisms underlying this phenomenon, we employed the Maxwell-Stefan equation to develop a 1D model and obtain a relation between the flux of solvents and the driving forces. Viscosity gradients are known to drive transport, but the development of an electrical current has not been theoretically described prior to this work.

FINDINGS

Our 1D model shows that the ionic current depends on the ideality of the solvent, though both ideal and non-ideal scenarios demonstrated good agreement with experimental data. We employed the model to understand the impact of solution bulk ionic strength and pH on the drift of ionic species with same reservoirs solution properties. Our modeling results unveiled the significant impact of bulk solution properties on the drift of ions which is in agreement with the experiments. Moreover, we have shown that the diffusion gradient along the nanochannel contributes significantly into driving ionic species if we even apply a small ionic concentration gradient to both reservoirs. Our modeling results may pave the way for finding novel applications for drift of ions in a diffusion gradient, which can be induced by connecting reservoirs of different viscosity fluids.

Ionic currents underlying different patterns of electrical activity in working cardiac myocytes of mammals and non-mammalian vertebrates

The orderly contraction of the vertebrate heart is determined by generation and propagation of cardiac action potentials (APs). APs are generated by the integrated activity of time- and voltage-dependent ionic channels which carry inward Na⁺ and Ca²⁺ currents, and outward K⁺ currents. This review compares atrial and ventricular APs and underlying ion currents between different taxa of vertebrates. We have collected literature data and attempted to find common electrophysiological features for two or more vertebrate groups, show differences between taxa and cardiac chambers, and indicate gaps in the existing data. Although electrical excitability of the heart in all vertebrates is based on the same superfamily of channels, there is a vast variability of AP waveforms between atrial and ventricular myocytes, between different species of the same vertebrate class and between endothermic and ectothermic animals. The wide variability of AP shapes is related to species-specific differences in animal size, heart rate, stage of ontogenetic development, excitation-contraction coupling, temperature and oxygen availability. Some of the differences between taxa are related to evolutionary development of genomes, which appear e.g. in the expression of different Na⁺ and K⁺ channel orthologues in cardiomyocytes of vertebrates. There is a wonderful variability of AP shapes and underlying ion currents with which electrical excitability of vertebrate heart can be generated depending on the intrinsic and extrinsic conditions of animal body. This multitude of ionic mechanisms provides excellent material for studying how the function of the vertebrate heart can adapt or acclimate to prevailing physiological and environmental conditions.

Voltage gated sodium channel inhibitors as anticonvulsant drugs: A systematic review on recent developments and structure activity relationship studies

Voltage-gated sodium channel blockers are one of the vital targets for the management of several central nervous system diseases, including epilepsy, chronic pain, psychiatric disorders, and spasticity. The voltage-gated sodium channels play a key role in controlling cellular excitability. This reduction in excitotoxicity is also applied to improve the symptoms of epileptic conditions. The effectiveness of antiepileptic drugs as sodium channel depends upon the reversible blocking of the spontaneous discharge without blocking its propagation. There are number of antiepileptic drug(s) which are in pipeline to flour the market to conquer abnormal neuronal excitability. They inhibit the seizures through the inhibition of complex voltage- and frequency-dependent ionic currents through sodium channels. Over the past decade, the sodium channel is one of the most explored targets to control or treat the seizure, but there has not been any game-changing discovery yet. Although there are large numbers of drugs approved for the treatment of epilepsy, however they are associated with several acute to chronic side effects. Many research groups have tirelessly worked for better therapeutic medication on this popular target to treat epileptic seizures. The review quotes briefly the developments of the approved examples of sodium channel blockers as anticonvulsant drugs. Medicinal chemists have tried the design and development of some more potent anticonvulsant drugs to minimize the toxicity that are discussed here, and an emphasis is given for their possible mechanism and the structure-activity relationship (SAR).

On-chip ionic current sensor

Neural implants that deliver drugs or electrical stimuli via microfluidic ports are promising in providing therapy for various disorders such as epilepsy, chronic pain, and vestibular diseases. To deliver the stimuli to a neural target, these devices incorporate two or more electrodes that apply an electric field to drive charged particles or ions along an aqueous route provided by microfluidic channels. The amount of drug/current delivered is determined by measuring the ionic current flow. When the ionic current can only travel from one electrode to another via a single route or channel, the amount of therapeutic current is stoichiometrically equal to the electronic current applied by the device and therefore can be measured with an electronic current sensor. However, some recently developed devices contain networks of branched channels. In this case, the presence of multiple parallel ionic current paths makes it so that the current through any one individual channel is no longer measurable by observing electronic current alone. Here, we present an on-chip sensor that uses two Pt/Ir electrodes to transduce the ionic current through a target channel into a measurable voltage signal. The size of the metal wires did not impact the measured voltage, the size of the channel between the two sensing electrodes determines sensitivity of the sensor, change in temperature can cause a change in readings, and input impedance of the voltage measuring equipment must be greater than 1 GΩ to maintain measurement stability. The sensor showed stability of reading in a one-week longevity test.

Ion channel reconstitution in lipid bilayers

Incorporation of ion channels in planar lipid bilayers allows detecting and measuring ion channel activity in a well-controlled system. This technique provides critical information about ion channel kinetics, ion selectivity, gating mechanism, open probability, unitary conductance, subconductance states, voltage dependence, and burst opening events, particularly at the single molecule level. Planar lipid bilayers provide a unique controllable environment that enables maintaining specific regulatory components, including lipids, ligands, inhibitors, particular ions, and proteins, as well as the temperature that can modulate activity of many ion channels. Thus, this system provides explicit details about ion channel gating mechanism and enables identifying its particular regulatory molecules or components. This chapter will describe the planar lipid bilayer method using the example of a transient receptor potential (TRP) ion channel family member. The planar lipid bilayer electrophysiological approach has proven to be useful in studying intrinsic properties of TRP channels. This method is particularly valuable for our understanding of intrinsic temperature sensitivity of thermoreceptors such as TRP channels and direct effects of TRP channels agonists, antagonists, co-factors, and other modifiers.

Discrimination of single-stranded DNA homopolymers by sieving out G-quadruplex using tiny solid-state nanopores

Nanopore sensor has been developed as a promising technology for DNA sequencing at the single-base resolution. However, the discrimination of homopolymers composed of guanines from other nucleotides has not been clearly revealed due to the easily formed G-quadruplex in aqueous buffers. In this work, we report that a tiny silicon nitride nanopore was used to sieve out G tetramers to make sure only homopolymers composed of guanines could translocate through the nanopore, then the 20-nucleotide long ssDNA homopolymers could be identified and differentiated. It is found that the size of the nucleotide plays a major role in affecting the current blockade as well as the dwell time while DNA is translocating through the nanopore. By the comparison of translocation behavior of ssDNA homopolymers composed of nucleotides with different volumes, it is found that smaller nucleotides can lead to higher translocation speed and lower current blockage, which is also found and validated for the 105-nucleotide long homopolymers. The studies performed in this work will improve our understanding of nanopore-based DNA sequencing at single-base level.

TRP Channel Reconstitution in Lipid Bilayers

The family of the transient receptor potential (TRP) proteins presents a diverse group of polymodal ion channels intertwined in the regulation of various physiological processes. Currently, TRP channels are well established in temperature-sensation, thermoregulation, pain sensation, and mineral homeostasis. Furthermore, new evidence suggests that TRP channels are also implicated in hormonal signaling, where the channels are responsible for propagating hormone-induced signals along the neural circuitry and also regulating cellular processes of nonexcitable cells. Due to this wide assortment of actions, TRP channels have been attracting immense scientific interest in various fields.In this chapter, I describe incorporation and characterization of several TRP channels using an electrophysiological approach known as planar lipid bilayers. This technique features measurements of functional activities of ion channels in a well-defined reconstituted system. The priority of this electrophysiological approach is identifying intrinsic properties of ion channels, which is particularly valuable in appreciating intrinsic temperature sensitivity concerning thermo-TRP channels, but also direct mechanisms of channels agonists, antagonists, cofactors, and other modifiers.

Diadenosine pentaphosphate affects electrical activity in guinea pig atrium via activation of potassium acetylcholine-dependent inward rectifier

Diadenosine pentaphosphate (Ap5A) belongs to the family of diadenosine polyphosphates, endogenously produced compounds that affect vascular tone and cardiac performance when released from platelets. The previous findings indicate that Ap5A shortens action potentials (APs) in rat myocardium via activation of purine P2 receptors. The present study demonstrates alternative mechanism of Ap5A electrophysiological effects found in guinea pig myocardium. Ap5A (10-4 M) shortens APs in guinea pig working atrial myocardium and slows down pacemaker activity in the sinoatrial node. P1 receptors antagonist DPCPX (10-7 M) or selective GIRK channels blocker tertiapin (10-6 M) completely abolished all Ap5A effects, while P2 blocker PPADS (10-4 M) was ineffective. Patch-clamp experiments revealed potassium inward rectifier current activated by Ap5A in guinea pig atrial myocytes. The current was abolished by DPCPX or tertiapin and therefore was considered as potassium acetylcholine-dependent inward rectifier (I KACh). Thus, unlike rat, in guinea pig atrium Ap5A produces activation of P1 receptors and subsequent opening of KACh channels leading to negative effects on cardiac electrical activity.

Single channel activity of OmpF-like porin from Yersinia pseudotuberculosis

To gain a mechanistic insight in the functioning of the OmpF-like porin from Yersinia pseudotuberculosis (YOmpF), we compared the effect of pH variation on the ion channel activity of the protein in planar lipid bilayers and its binding to lipid membranes. The behavior of YOmpF channels upon acidification was similar to that previously described for Escherichia coli OmpF. In particular, a decrease in pH of the bathing solution resulted in a substantial reduction of YOmpF single channel conductance, accompanied by the emergence of subconductance states. Similar subconductance substates were elicited by the addition of lysophosphatidylcholine. This observation, made with porin channels for the first time, pointed to the relevance of lipid-protein interactions, in particular, the lipid curvature stress, to the appearance of subconductance states at acidic pH. Binding of YOmpF to membranes displayed rather modest dependence on pH, whereas the channel-forming potency of the protein tremendously decreased upon acidification.

Surface charge modulated aptasensor in a single glass conical nanopore

In this work, we have proposed a label-free nanopore-based biosensing strategy for protein detection by performing the DNA-protein interaction inside a single glass conical nanopore. A lysozyme binding aptamer (LBA) was used to functionalize the walls of glass nanopore via siloxane chemistry and negatively charged recognition sites were thus generated. The covalent modification procedures and their recognition towards lysozyme of the single conical nanopore were characterized via ionic current passing through the nanopore membrane, which was measured by recording the current-voltage (I-V) curves in 1mM KCl electrolyte at pH=7.4. With the occurring of recognition event, the negatively charged wall was partially neutralized by the positively charged lysozyme molecules, leading to a sensitive change of the surface charge-dependent current-voltage (I-V) characteristics. Our results not only demonstrate excellent selectivity and sensitivity towards the target protein, but also suggest a route to extend this nanopore-based sensing strategy to the biosensing platform designs of a wide range of proteins based on a charge modulation.

Influence of mechanical stress on fibroblast-myocyte interactions in mammalian heart

Cardiac fibroblasts are an essential component of cardiac tissue. These cells not only produce the extracellular matrix, but also are electrically and mechanically coupled with cardiomyocytes. In this way, fibroblasts can influence the electrical activity of cardiomyocytes. Cardiac fibroblasts cannot generate action potentials, but their membrane potential is controlled by mechanical stretch or compression of the surrounding myocardium which in turn affects their interaction with myocytes and the way myocytes respond to mechanical stress. This review discusses the electrical properties of cardiac fibroblasts, the present evidence of fibroblast-myocyte coupling and the way in which these cells respond to mechanical stress. This article is part of a Special Issue entitled "Myocyte-Fibroblast Signalling in Myocardium."