Concentration polarization in translocation of DNA through nanopores and nanochannels

Engineering inlet structures to enhance DNA capture into nanochannels in a polymer nanofluidic device produced via nanoimprint lithography

Operating nanofluidic biosensors requires threading single molecules to be analyzed from microfluidic networks into nanostructures, mostly nanochannels or nanopores. Different inlet structures have been employed as a means of enhancing the number of the capture events into nanostructures. Here, we systematically investigated the effects of various engineered inlet structures formed at the micro/nanochannel interface on the capture of single λ-DNA molecules into the nanochannels. Different inlet geometries were evaluated and ranked in order of their effectiveness. Adding an inlet structure prior to a nanochannel effectively improved the DNA capture rate by 190 - 700 % relative to that for the abrupt micro/nanochannel interface. The capture of DNA from the microchannel to various inlets was determined mainly by the capture volumes of the inlet structures and the geometrically modified electric field in the inlet structure. However, as the width of the inlet structure increased, the hydrodynamic flow existing in the microchannel negatively influenced the DNA capture by dragging some DNA molecules deep into the inlet structure back to the microchannel. Our results indicate that engineering inlet structures is an effective means of controlling the capture of DNA molecules into nanostructures, which is important for operation of nanofluidic biosensors.

Protein and DNA Yield Current Enhancements, Slow Translocations, and an Enhanced Signal-to-Noise Ratio under a Salt Imbalance

Nanopores are a promising single-molecule sensing device class that captures molecular-level information through resistive or conductive pulse sensing (RPS and CPS). The latter has not been routinely utilized in the nanopore field despite the benefits it could provide, specifically in detecting subpopulations of a molecule. A systematic study was conducted here to study the CPS-based molecular discrimination and its voltage-dependent characteristics. CPS was observed when the cation movement along both electrical and chemical gradients was favored, which led to an ∼3× improvement in SNR (i.e., signal-to-noise ratio) and an ∼8× increase in translocation time. Interestingly, a reversal of the salt gradient reinstates the more conventional resistive pulses and may help elucidate RPS-CPS transitions. The asymmetric salt conditions greatly enhanced the discrimination of DNA configurations including linear, partially folded, and completely folded DNA states, which could help detect subpopulations in other molecular systems. These findings were then utilized for the detection of a Cas9 mutant, Cas9d10a─a protein with broad utilities in genetic engineering and immunology─bound to DNA target strands and the unbound Cas9d10a + sgRNA complexes, also showing significantly longer event durations (>1 ms) than typically observed for proteins.

Investigation of entrance effects on particle electrophoretic behavior near a nanopore for resistive pulse sensing

Resistive pulse sensing using solid-state nanopores provides a unique platform for detecting the structure and concentration of molecules of different types of analytes in an electrolyte solution. The capture of an entity into a nanopore is subject not only to the electrostatic force but also the effect of electroosmotic flow originating from the charged nanopore surface. In this study, we theoretically analyze spherical particle electrophoretic behavior near the entrance of a charged nanopore. By investigating the effects of pore size, particle-pore distance, and salt concentration on particle velocity, we summarize dominant mechanisms governing particle behavior for a range of conditions. In the literature, the Helmholtz-Smoluchowski equation is often adopted to evaluate particle translocation by considering the zeta potential difference between the particle and nanopore surfaces. We point out that, due to the difference of the electric field inside and outside the nanopore and the influence from the existence of the particle itself, the zeta potential of the particle, however, needs to be at least 30% higher than that of the nanopore to allow the particle to enter into the nanopore when its velocity is close to zero. Accordingly, we summarize the effective salt concentrations that enable successful particle capture and detection for different pore sizes, offering direct guidance for nanopore applications.

Biphasic signals during nanopore translocation of DNA and nanoparticles due to strong ion cloud deformation

We report a theory for biphasic ionic current signals during DNA and nanoparticle translocation through a solid-state nanopore that produces scaling results consistent with those of finite element simulations (FEM), molecular dynamics (MD) simulations and experiments. For standard nanopores designed for potential rapid sequencing applications, the electric field is enhanced by orders of magnitude due to field focusing and can severely deform the ion-cloud around the charged DNA. Highly fore-aft asymmetric space charge distribution leads to a universal quasi-steady comet-like structure with a long tail. In contrast to previous biphasic theories, the charge density and length of the tail, which are responsible for the negative resistive pulse, are shown to depend sensitively on the dimensionless applied field, the Peclet number Pe, with a ∓1 scaling, due to a balance between tangential migration and normal diffusion. An optimum Pe is predicted where the negative pulse has the maximum amplitude.

Characterization and manipulation of single nanoparticles using a nanopore-based electrokinetic tweezer

Manipulation and characterization of nanoscale objects through electrokinetic techniques offer numerous advantages compared to the existing optical methods and hold great potential for both fundamental research and practical applications. Here we present a novel electrokinetic tweezer for single nanoparticle manipulation and characterization based on electrokinetic trapping near a low-aspect-ratio nanopore. We find that this nanopore-based electrokinetic tweezer share lots of similarity with optical tweezers and can be modeled as an overdamped harmonic oscillator, with the spring constant of the system being the trap stiffness. We show that different values of ionic currents through the nanopore and trap stiffnesses are achieved when trapping nanoparticles with different sizes (down to 100 nm) and/or zeta potentials. We also demonstrate that the trap stiffness and nanoparticle position can be easily tuned by changing the applied voltage and buffer concentration. We envision that further development of this electrokinetic tweezer will enable various advanced tools for nanophotonics, drug delivery, and biosensing.

Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement

We report that long double-stranded DNA confined to quasi-1D nanochannels undergoes superdiffusive motion under the action of the enzyme T4 DNA ligase in the presence of necessary co-factors. Inside the confined environment of the nanochannel, double-stranded DNA molecules stretch out due to self-avoiding interactions. In absence of a catalytically active enzyme, we see classical diffusion of the center of mass. However, cooperative interactions of proteins with the DNA can lead to directed motion of DNA molecules inside the nanochannel. Here we show directed motion in this configuration for three different proteins (T4 DNA ligase, MutS, E. coli DNA ligase) in the presence of their energetic co-factors (ATP, NAD⁺).

Entrance Effects Induced Rectified Ionic Transport in a Nanopore/Channel

The nanofluidic diode, as one of the emerging nanofluidic logic devices, has been used in many fields such as biosensors, energy harvesting, and so on. However, the entrance effects of the nanofluidic ionic conductance were less discussed, which can be a crucial factor for the ionic conduction. Here we calculate the ionic conductance as a function of the length-to-pore ratio (L/r), which has a clear boundary between nanopore (surface dominated) and nanochannel (geometry dominated) electrically in diluted salt solution. These entrance effects are even more obvious in the rectified ionic conduction with oppositely charged exterior surfaces of a nanopore. We build three models-Exterior Charged Surface model (ECS), Inner Charged Surface model (ICS), and All Charged Surface model (ACS)-to discuss the entrance effects on the ionic conduction. Our results demonstrate, for a thin nanopore, that the ECS model has a larger ionic rectification factor (Q) than that of ICS model, with a totally reversed tendency of Q compared to the ICS and ACS models as L/r increases. Our models predict an alternative option of building nanofluidic biosensors that only need to modify the exterior surface of a nanopore, avoiding the slow diffusion of molecules in the nanochannel.

MD Study of Solution Concentrations on Ion Distribution in a Nanopore-Based Device Inspired from Red Blood Cells

A molecular dynamics model of a nanopore-based device, which is similar to the nanopores in a cell membrane, was used to determine the influence of solution concentration on radial ion distribution, screening effects, and the radial potential profile in the nanopore. Results from these simulations indicate that as the solution concentration increases, the density peaks for both the counterion and coion near the charged wall increase at different speeds as screening effects appeared. Consequently, the potential near the charged wall of the nanopore changed from negative to positive during the simulation. The detailed understanding of ion distribution in nanopores is important for controlling the ion permeability and improving the cell transfection and also the design and application of nanofluidic devices.

Quantification of Vortex Generation Due to Non-Equilibrium Electrokinetics at the Micro/Nanochannel Interface: Particle Tracking Velocimetry

We describe a quantitative study of vortex generation due to non-equilibrium electrokinetics near a micro/nanochannel interface. The microfluidic device is comprised of a microchannel with a set of nanochannels. These perm-selective nanochannels induce flow instability and thereby produce strong vortex generation. We performed tracking visualization of fluorescent microparticles to obtain velocity fields. Particle tracking enables the calculation of an averaged velocity field and the velocity fluctuations. We characterized the effect of applied voltages and electrolyte concentrations on vortex formation. The experimental results show that an increasing voltage or decreasing concentration results in a larger vortex region and a strong velocity fluctuation. We calculate the normalized velocity fluctuation-whose meaning is comparable to turbulent intensity-and we found that it is as high as 0.12. This value is indicative of very efficient mixing, albeit with a small Reynolds number.

Influence of concentration polarization on DNA translocation through a nanopore

Concentration polarization can be induced by the unique ion-perm selectivity of small nanopores, leading to a salt concentration gradient across nanopores. This concentration gradient can create diffusio-osmosis and induce an electric field, affecting ionic currents on DNA that translocates through a nanopore. Here this influence is theoretically investigated by solving the continuum Poisson-Nernst-Planck model for different salt concentrations, DNA surface charge densities, and pore properties. By implementing the perturbation method, we can explicitly compute the contribution of concentration polarization to the ionic current. The induced electric field by concentration polarization is opposite to the imposed electric field and decreases the migration current, and the induced diffusio-osmosis can decrease the convection current as well. Our studies suggest that the importance of the concentration polarization can be determined by the parameter λ/G where λ is the double-layer thickness and G is the gap size. When λ/G is larger than a critical value, the influence of concentration polarization becomes more prominent. This conclusion is supported by the studies on the dependence of the ionic current on salt concentration and pore properties, showing that the difference between two models with and without accounting for concentration polarization is larger for low salts and small pores, which correspond to larger λ/G.

Collapse of DNA under alternating electric fields

Recent studies have shown that double-stranded DNA can collapse in the presence of a strong electric field. Here we provide an in-depth study of the collapse of DNA under weak confinement in microchannels as a function of buffer strength, driving frequency, applied electric-field strength, and molecule size. We find that the critical electric field at which DNA molecules collapse (tens of kV/m) is strongly dependent on driving frequency (100-800 Hz) and molecular size (20-160 kbp), and weakly dependent on the ionic strength (8-60 mM). We argue that an apparent stretching at very high electric fields is an artifact of the finite frame time of video microscopy.

Electro-osmotic pumping and ion-concentration polarization based on conical nanopores

A numerical investigation is performed into the characteristics of an electro-osmotic pump consisting of a negatively charged conical nanopore. It is shown that the dependence of the flow rectification effect on the bias direction is the reverse of that of the ion current rectification effect. Moreover, the nozzle mode (i.e., the bias is applied from the base side of the nanopore to the tip side) has a higher flow rate compared to the diffuser mode (i.e., the bias is applied from the tip side of the nanopore to the base side). The results showed that the ion-concentration polarization effect occurred inside the conical nanopore, resulting in surface conduction dominating in the ionic current. The ions inside the nanopore are depleted and enriched under the nozzle mode and the diffuser mode, respectively. As a result, the electro-osmotic pump yields a greater pumping pressure, flow rate, and energy conversion efficiency when operating in the nozzle mode. In addition, we also investigated the flow rate rectification behavior for the conical nanopore. The best flow rate rectification factor in this work is 2.06 for an electrolyte concentration of 10(-3) M.

Hydrodynamic slip on DNA observed by optical tweezers-controlled translocation experiments with solid-state and lipid-coated nanopores

We use optical tweezers to investigate the threading force on a single dsDNA molecule inside silicon-nitride nanopores between 6 and 70 nm in diameter, as well as lipid-coated solid-state nanopores. We observe a strong increase of the threading force for decreasing nanopore size that can be attributed to a significant reduction in the electroosmotic flow (EOF), which opposes the electrophoresis. Additionally, we show that the EOF can also be reduced by coating the nanopore wall with an electrically neutral lipid bilayer, resulting in an 85% increase in threading force. All experimental findings can be described by a quantitative theoretical model that incorporates a hydrodynamic slip effect on the DNA surface with a slip length of 0.5 nm.

Effect of finite ion sizes in an electrostatic potential distribution for a charged soft surface in contact with an electrolyte solution

We provide a theory to analyze the impact of finite ion sizes (or steric effect) in electrostatic potential distribution for a charged soft surface in contact with an electrolyte solution. The theory is based on a free energy model that appropriately accounts for the contribution of finite ion sizes as well as the structural characteristics of a soft interface, represented by a combination of a rigid surface and a fixed charge layer (FCL), with the FCL being in contact with an electrolyte solution forming an electric double layer (EDL). This FCL contains a particular kind of ion which is impermeable to the electrolyte solution, and this impermeability is quantified in terms of the corresponding Donnan potential of the "membrane" represented by the FCL-electrolyte interface. We find that consideration of the finite ion size increases the magnitude of this Donnan potential, with the extent of increase being dictated by three length scales, namely, the thickness of the FCL, the thickness of the electrolyte EDL, and the thickness of an equivalent EDL within the FCL. Such regulation of the Donnan potential strongly affects the distribution of the permeable electrolyte ions within the FCL, which in turn will have significant implications in several processes involving "soft" biological membranes.

Detecting a single molecule using a micropore-nanopore hybrid chip

Nanopore-based DNA sequencing and biomolecule sensing have attracted more and more attention. In this work, novel sensing devices were built on the basis of the chips containing nanopore arrays in polycarbonate (PC) membranes and micropores in Si3N4 films. Using the integrated chips, the transmembrane ionic current induced by biomolecule's translocation was recorded and analyzed, which suggested that the detected current did not change linearly as commonly expected with increasing biomolecule concentration. On the other hand, detailed translocation information (such as translocation gesture) was also extracted from the discrete current blockages in basic current curves. These results indicated that the nanofluidic device based on the chips integrated by micropores and nanopores possessed comparative potentials in biomolecule sensing.

Electrodiffusion kinetics of ionic transport in a simple membrane channel

We employ numerical techniques for solving time-dependent full Poisson-Nernst-Planck (PNP) equations in 2D to analyze transient behavior of a simple ion channel subject to a sudden electric potential jump across the membrane (voltage clamp). Calculated spatiotemporal profiles of the ionic concentrations and electric potential show that two principal exponential processes can be distinguished in the electrodiffusion kinetics, in agreement with original Planck's predictions. The initial fast process corresponds to the dielectric relaxation, while the steady state is approached in a second slower exponential process attributed to the nonlinear ionic redistribution. Effects of the model parameters such as the channel length, height of the potential step, boundary concentrations, permittivity of the channel interior, and ionic mobilities on electrodiffusion kinetics are studied. Numerical solutions are used to determine spatiotemporal profiles of the electric field, ionic fluxes, and both the conductive and displacement currents. We demonstrate that the displacement current is a significant transient component of the total electric current through the channel. The presented results provide additional information about the classical voltage-clamp problem and offer further physical insights into the mechanism of electrodiffusion. The used numerical approach can be readily extended to multi-ionic models with a more structured domain geometry in 2D or 3D, and it is directly applicable to other systems, such as synthetic nanopores, nanofluidic channels, and nanopipettes.

Reluctance of a neutral nanoparticle to enter a charged pore

We consider the translocation of a neutral (uncharged) nanoparticle through a pore in a thin membrane with constant surface charge density. If the concomitant Debye screening layer is sufficiently thin, the resulting forces experienced by the particle on its way through the pore are negligible. But when the Debye length becomes comparable to the pore diameter, the particle encounters a quite significant potential barrier while approaching and entering the pore, and symmetrically upon exiting the pore. The main reason is an increasing pressure, which acts on the particle when it intrudes into the counter ion cloud of the Debye screening layer. In case the polarizability of the particle is different (usually smaller) than that of the ambient fluid, a second, much smaller contribution to the potential barrier is due to self-energy effects. Our numerical treatment of the problem is complemented by analytical approximations for sufficiently long cylindrical particles and pores, which agree very well with the numerics.

Slow translocation of polynucleotides and their discrimination by α-hemolysin inside a single track-etched nanopore designed by atomic layer deposition

We report the formation of a hybrid biological/artificial nanopore by the direct insertion of non-modified α-hemolysin at the entrance of a high aspect ratio (length/diameter) biomimetic nanopore. In this robust hybrid system, the protein exhibits the same polynucleotide discrimination properties as in the biological membrane and the polynucleotide dwell time is strongly increased. This nanopore is very promising for DNA sequencing applications where the high DNA translocation velocity and the fragility of the support are the main bottlenecks.

Exploring new scaling regimes for streaming potential and electroviscous effects in a nanocapillary with overlapping electric double layers

In this paper, we unravel new scaling regimes for streaming potential and electroviscous effects in a nanocapillary with thick overlapping Electric Double Layers (EDLs). We observe that the streaming potential, for a given value of the capillary zeta (ζ) potential, varies with the EDL thickness and a dimensionless parameter R, quantifying the conduction current. Depending on the value of R, variation of the streaming potential with the EDL thickness demonstrates distinct scaling regimes: one can witness a Quadratic Regime where the streaming potential varies as the square of the EDL thickness, a Weak Regime where the streaming potential shows a weaker variation with the EDL thickness, and a Saturation Regime where the streaming potential ceases to vary with the EDL thickness. Effective viscosity, characterizing the electroviscous effect, obeys the variation of the streaming potential for smaller EDL thickness values; however, for larger EDL thickness the electroosmotic flow profile dictates the electroviscous effect, with insignificant contribution of the streaming potential.

Single-molecule studies of intrinsically disordered proteins using solid-state nanopores

Partially or fully disordered proteins are instrumental for signal-transduction pathways; however, many mechanistic aspects of these proteins are not well-understood. For example, the number and nature of intermediate states along the binding pathway is still a topic of intense debate. To shed light on the conformational heterogeneity of disordered protein domains and their complexes, we performed single-molecule experiments by translocating disordered proteins through a nanopore embedded within a thin dielectric membrane. This platform allows for single-molecule statistics to be generated without the need of fluorescent labels or other modification groups. These studies were performed on two different intrinsically disordered protein domains, a binding domain from activator of thyroid hormone and retinoid receptors (ACTR) and the nuclear coactivator binding domain of CREB-binding protein (NCBD), along with their bimolecular complex. Our results demonstrate that both ACTR and NCBD populate distinct conformations upon translocation through the nanopore. The folded complex of the two disordered domains, on the other hand, translocated as one conformation. Somewhat surprisingly, we found that NCBD undergoes a charge reversal under high salt concentrations. This was verified by both translocation statistics as well as by measuring the ζ-potential. Electrostatic interactions have been previously suggested to play a key role in the association of intrinsically disordered proteins, and the observed behavior adds further complexity to their binding reactions.

Spatiotemporal mapping of concentration polarization induced pH changes at nanoconstrictions

Under an applied electric field, concentration polarization (CP) arises from ion permselectivity of most nanoporous materials and biological ion channels. We present novel methods to quantitatively assess CP-induced spatiotemporal changes of pH that may significantly impact transport dynamics, device functionality, and physicochemical properties of molecular analytes in devices with nanofluidic constrictions. We measured pH fluctuations of >1.5 pH units and changes extending over 100's of micrometers from nanoconstrictions. The degree of change depends on key system parameters including buffer composition, surface charge, and strength of electric field. The results highlight the importance of neglected contributions of pH changes, and the approach can aid characterization and manipulation of mass transport in nanofluidic systems.