Electrophoretic transport of biomolecules through carbon nanotube membranes

Electrophoretic transport of proteins across electrochemically oxidized multi-walled carbon nanotube (MWCNT) membranes has been investigated. A small charged protein, lysozyme, was successfully pumped across MWCNT membranes by an electric field while rejecting larger bovine serum albumin (BSA). Transport of lysozome was reduced by a factor of about 30 in comparison to bulk mobility and consistent with the prediction for hindered transport. Mobilities between 0.33 and 1.4 × 10(-9) m(2) V(-1) s(-1) were observed and are approximately 10-fold faster than comparable ordered nanoporous membranes and consistent with continuum models. For mixtures of BSA and lysozyme, complete rejection of BSA is seen with electrophoretic separations.

Redesign of a plugged beta-barrel membrane protein

The redesign of biological nanopores is focused on bacterial outer membrane proteins and pore-forming toxins, because their robust β-barrel structure makes them the best choice for developing stochastic biosensing elements. Using membrane protein engineering and single-channel electrical recordings, we explored the ferric hydroxamate uptake component A (FhuA), a monomeric 22-stranded β-barrel protein from the outer membrane of Escherichia coli. FhuA has a luminal cross-section of 3.1 × 4.4 nm and is filled by a globular N-terminal cork domain. Various redesigned FhuA proteins were investigated, including single, double, and multiple deletions of the large extracellular loops and the cork domain. We identified four large extracellular loops that partially occlude the lumen when the cork domain is removed. The newly engineered protein, FhuAΔC/Δ4L, was the result of a removal of almost one-third of the total number of amino acids of the wild-type FhuA (WT-FhuA) protein. This extensive protein engineering encompassed the entire cork domain and four extracellular loops. Remarkably, FhuAΔC/Δ4L forms a functional open pore in planar lipid bilayers, with a measured unitary conductance of ∼4.8 nanosiemens, which is much greater than the values recorded previously with other engineered FhuA protein channels. There are numerous advantages and prospects of using such an engineered outer membrane protein not only in fundamental studies of membrane protein folding and design, and the mechanisms of ion conductance and gating, but also in more applicative areas of stochastic single-molecule sensing of proteins and nucleic acids.

Distinguishable populations report on the interactions of single DNA molecules with solid-state nanopores

Solid-state nanopores have received increasing interest over recent years because of their potential for genomic screening and sequencing. In particular, small nanopores (2-5 nm in diameter) allow the detection of local structure along biological molecules, such as proteins bound to DNA or possibly the secondary structure of RNA molecules. In a typical experiment, individual molecules are translocated through a single nanopore, thereby causing a small deviation in the ionic conductance. A correct interpretation of these conductance changes is essential for our understanding of the process of translocation, and for further sophistication of this technique. Here, we present translocation measurements of double-stranded DNA through nanopores down to the diameter of the DNA itself (1.8-7 nm at the narrowest constriction). In contrast to previous findings on such small nanopores, we find that single molecules interacting with these pores can cause three distinct levels of conductance blockades. We attribute the smallest conductance blockades to molecules that briefly skim the nanopore entrance without translocating, the intermediate level of conductance blockade to regular head-to-tail translocations, and the largest conductance blockades to obstruction of the nanopore entrance by one or multiple (duplex) DNA strands. Our measurements are an important step toward understanding the conductance blockade of biomolecules in such small nanopores, which will be essential for future applications involving solid-state nanopores.

Electrokinetic particle translocation through a nanopore

Nanoparticle electrophoretic translocation through a single nanopore induces a detectable change in the ionic current, which enables the nanopore-based sensing for various bio-analytical applications. In this study, a transient continuum-based model is developed for the first time to investigate the electrokinetic particle translocation through a nanopore by solving the Nernst-Planck equations for the ionic concentrations, the Poisson equation for the electric potential and the Navier-Stokes equations for the flow field using an arbitrary Lagrangian-Eulerian (ALE) method. When the applied electric field is relatively low, a current blockade is expected. In addition, the particle could be trapped at the entrance of the nanopore when the electrical double layer (EDL) adjacent to the charged particle is relatively thick. When the electric field imposed is relatively high, the particle can always pass through the nanopore by electrophoresis. However, a current enhancement is predicted if the EDL of the particle is relatively thick. The obtained numerical results qualitatively agree with the existing experimental results. It is also found that the initial orientation of the particle could significantly affect the particle translocation and the ionic current through a nanopore. Furthermore, a relatively high electric field tends to align the particle with its longest axis parallel to the local electric field. However, the particle's initial lateral offset from the centerline of the nanopore acts as a minor effect.

Pink noise of ionic conductance through single artificial nanopores revisited

We report voltage-clamp measurements through single conical nanopore obtained by chemical etching of a single ion track in polyimide film. Special attention is paid to the pink noise of the ionic current (i.e., 1/f noise) measured with different filling liquids. The relative pink-noise amplitude is almost independent of concentration and pH for KCl solutions, but varies strongly using ionic liquids. In particular, we show that depending on the ionic liquid, the transport of charge carriers is strongly facilitated (low noise and higher conductivity than in the bulk) or jammed. These results show that the origin of the pink noise can be ascribed neither to fluctuations of the pore geometry nor to the pore wall charges, but rather to a cooperative effect on ions motion in confined geometry.

Determining nanocapillary geometry from electrochemical impedance spectroscopy using a variable topology network circuit model

Solid-state nanopores and nanocapillaries find increasing use in a variety of applications including DNA sequencing, synthetic nanopores, next-generation membranes for water purification, and other nanofluidic structures. This paper develops the use of electrochemical impedance spectroscopy to determine the geometry of nanocapillaries. A network equivalent circuit element is derived to include the effects of the capacitive double layer inside the nanocapillaries as well as the influence of varying nanocapillary radius. This variable topology function is similar to the finite Warburg impedance in certain limits. Analytical expressions for several different nanocapillary shapes are derived. The functions are evaluated to determine how the impedance signals will change with different nanocapillary aspect ratios and different degrees of constriction or inflation at the capillary center. Next, the complex impedance spectrum of a nanocapillary array membrane is measured at varying concentrations of electrolyte to separate the effects of nanocapillary double layer capacitance from those of nanocapillary geometry. The variable topology equivalent circuit element model of the nanocapillary is used in an equivalent circuit model that included contributions from the membrane and the measurement apparatus. The resulting values are consistent with the manufacturer's specified tolerances of the nanocapillary geometry. It is demonstrated that electrochemical impedance spectroscopy can be used as a tool for in situ determination of the geometry of nanocapillaries.

Multiplexed parallel single transport recordings on nanopore arrays

We introduce a nanofabricated silicon chip for massively multiplexed analysis of membrane channels and transporters in suspended lipid membranes that does not require any surface modification or organic solvent. Transport processes through single membrane complexes are monitored by fluorescence. The chip consists of an array of well-defined nanopores, addressing an individual pyramidal back-reflecting 30-fL compartment. The setup allows simultaneous analyses of ∼1,000 single transmembrane events in one field of view, observing translocation kinetics of transmembrane complexes.

DNA strands attached inside single conical nanopores: ionic pore characteristics and insight into DNA biophysics

Single nanopores attract a great deal of scientific interest as a basis for biosensors and as a system to study the interactions and behavior of molecules in a confined volume. Tuning the geometry and surface chemistry of nanopores helps create devices that control transport of ions and molecules in solution. Here, we present single conically shaped nanopores whose narrow opening of 8 or 12 nm is modified with single-stranded DNA molecules. We find that the DNA occludes the narrow opening of nanopores and that the blockade extent decreases with the ionic strength of the background electrolyte. The results are explained by the ionic strength dependence of the persistence length of DNA. At low KCl concentrations (10 mM) the molecules assume an extended and rigid conformation, thereby blocking the pore lumen and reducing the flow of ionic current to a greater extent than compacted DNA at high salt concentrations. Attaching flexible polymers to the pore walls hence creates a system with tunable opening diameters in order to regulate transport of both neutral and charged species.

A nanochannel array-based electrochemical device for quantitative label-free DNA analysis

A strategy for label-free oligonucleotide (DNA) analysis has been proposed by measuring the DNA-morpholino hybridization hindered diffusion flux of probe ions Fe(CN)(6)(3-) through nanochannels of a porous anodic alumina (PAA) membrane. The flux of Fe(CN)(6)(3-) passing through the PAA nanochannels is recorded using an Au film electrochemical detector sputtered at the end of the nanochannels. Hybridization of the end-tethered morpholino in the nanochannel with DNA forms a negatively charged DNA-morpholino complex, which hinders the diffusion of Fe(CN)(6)(3-) through the nanochannels and results in a decreased flux. This flux is strongly dependent on ionic strength, nanochannel aperture, and target DNA concentration, which indicates a synergetic effect of steric and electrostatic repulsion effects in the confined nanochannels. Further comparison of the probe flux with different charge passing through the nanochannels confirms that the electrostatic effect between the probe ions and DNA dominates the hindered diffusion process. Under optimal conditions, the present nanochannel array-based DNA biosensor gives a detection limit of 0.1 nM.

Reversible cobalt ion binding to imidazole-modified nanopipettes

In this report, we demonstrate that quartz nanopipettes modified with an imidazole-terminated silane respond to metal ions (Co(2+)) in solution. The response of nanopipettes is evaluated through examination of the ion current rectification ratio. When nanopipettes are cycled between solutions of different pH, adsorbed Co(2+) can be released from the nanopipette surface, to regenerate binding sites of the nanopipette. These results demonstrate that rectification-based sensing strategies for nanopore sensors can benefit from selection of recognition elements with intermediate binding affinities, such that reversible responses can be attained.

Mathematical modeling and simulation of nanopore blocking by precipitation

High surface charges of polymer pore walls and applied electric fields can lead to the formation and subsequent dissolution of precipitates in nanopores. These precipitates block the pore, leading to current fluctuations. We present an extended Poisson-Nernst-Planck system which includes chemical reactions of precipitation and dissolution. We discuss the mathematical modeling and present 2D numerical simulations.

Fabrication and electrical characterization of a pore-cavity-pore device

We present a solid state nanopore device structure comprising two nanopores which are stacked above each other and connected via a pyramidal cavity of 10 fl volume. The process of fabrication of the pore-cavity-pore device (PCP) relies on the formation of one pore in a Si(3)N(4) membrane by electron beam lithography, while the other pore is chemically etched into the Si carrier by a feedback controlled process. The dimensions of the two nanopores as well as the cavity can be adjusted independently, which is confirmed by transmission electron microscopy. The PCP device is characterized with respect to its electrical properties, including noise analysis and impedance spectroscopy. An equivalent circuit model is identified and resistance, capacitance, and dielectric loss factors are obtained. Potential and electric field distributions inside the electrically biased device are simulated by finite element methods. The low noise characteristics of the PCP device (comparable to a single solid state nanopore) make it suitable for the stochastic sensing of single molecules; moreover, the pore-cavity-pore architecture allows for novel kinds of experiments including the trapping of single nano-objects and single molecule time-of-flight measurements.

Translocation events in a single walled carbon nanotube

Translocation of DNA oligomers through a single walled carbon nanotube was demonstrated recently. Translocation events are accompanied by giant current pulses, the origin of which remains obscure. Here, we show that introduction of a nucleotide alone, guanosine triphosphate into the input reservoir of a carbon nanotube nanofluidic also gives giant current pulses. Taken together with data on oligomer translocation, theses new results suggest that pulse width has a non-linear, power-law dependence on the number of nucleotides in a DNA molecule. We have also measured the time for the onset of DNA translocation pulses after bias reversal, finding that the time for the onset of translocation is directly proportional to the period of bias reversal.

Electrically sensing protease activity with nanopores

The enzymatic activity of a protease was electrically detected using nanopore recordings. A peptide substrate was tethered to microscale beads, and cleavage by the enzyme trypsin released a soluble fragment that was electrophoretically driven through the α-hemolysin protein pore, leading to detectable blockades in the ionic current. Owing to its simplicity, this approach to sense enzymatic activity may be applied to other proteases.

Evidence that small proteins translocate through silicon nitride pores in a folded conformation

The interaction of three proteins (histidine-containing phosphocarrier protein, HPr, calmodulin, CaM, and maltose binding protein, MBP) with synthetic silicon nitride (SiN(x)) membranes has been studied. The proteins which have a net negative charge were electrophoretically driven into pores of 7 and 5 nm diameter with a nominal length of 15 nm. The % blockade current and event duration were measured at three different voltages. For a translocation event it was expected that the % block would be constant with voltage whilst the event duration would decrease with increasing voltage. On the basis of these criteria, we deduce that MBP whose largest dimension is 6.5 nm does not translocate whereas up to 40% of CaM molecules can translocate the 7 nm pore as can a majority of HPr molecules, with some translocations being observed for the 5 nm pore. For translocation events the magnitude of the % blockade current is consistent with a folded conformation of the proteins surrounded by a hydration shell of 0.5-1.0 nm.

Dynamic translocation of ligand-complexed DNA through solid-state nanopores with optical tweezers

We investigated the threading and controlled translocation of individual lambda-DNA (λ-DNA) molecules through solid-state nanopores with piconewton force sensitivity, millisecond time resolution and picoampere ionic current sensitivity with a set-up combining quantitative 3D optical tweezers (OT) with electrophysiology. With our virtually interference-free OT set-up the binding of RecA and single peroxiredoxin protein molecules to λ-DNA was quantitatively investigated during dynamic translocation experiments where effective forces and respective ionic currents of the threaded DNA molecule through the nanopore were measured during inward and outward sliding. Membrane voltage-dependent experiments of reversible single protein/DNA translocation scans yield hysteresis-free, asymmetric single-molecule fingerprints in the measured force and conductance signals that can be attributed to the interplay of optical trap and electrostatic nanopore potentials. These experiments allow an exact localization of the bound protein along the DNA strand and open fascinating applications for label-free detection of DNA-binding ligands, where structural and positional binding phenomena can be investigated at a single-molecule level.

Electrical characterization of DNA-functionalized solid state nanopores for bio-sensing

We present data concerning the electrical properties of a class of biosensor devices based on bio-functionalized solid state nanopores able to detect different kinds of interactions between probe molecules, chemically attached to the pore surface, and target molecules present in solution and electrophoretically drawn through the nanometric channel. The great potentiality of this approach resides in the fact that the functionalization of a quite large pore (up to 50-60 nm) allows a sufficient diameter reduction for the attainment of a single molecule sensing dimension and selective activation, without the need for further material deposition, such as metal or oxides, or localized surface modification. The results indicate that it will be possible, in the near future, to conceive and design devices for parallel analysis of biological samples made of arrays of nanopores differently functionalized, fabricated by standard lithographic techniques, with important applications in the field of molecular diagnosis.

Changes in ion channel geometry resolved to sub-ångström precision via single molecule mass spectrometry

The ion channel formed by Staphylococcus aureus alpha-hemolysin switches between multiple open conducting states. We describe a method for precisely estimating the changes in the ion channel geometry that correspond to these different states. Experimentally, we observed that the permeability of a single channel to differently sized poly(ethylene glycol) molecules depends on the magnitude of the open state conductance. A simple theory is proposed for determining changes in channel length of 4.2% and in cross-sectional area of -0.4%.

Detection of urea-induced internal denaturation of dsDNA using solid-state nanopores

The ability to detect and measure dsDNA thermal fluctuations is of immense importance in understanding the underlying mechanisms responsible for transcription and replication regulation. We describe here the ability of solid-state nanopores to detect sub-nanometer changes in DNA structure as a result of chemically enhanced thermal fluctuations. In this study, we investigate the subtle changes in the mean effective diameter of a dsDNA molecule with 3-5 nm solid-state nanopores as a function of urea concentration and the DNA's AT content. Our studies reveal an increase in the mean effective diameter of a DNA molecule of approximately 0.6 nm at 8.7 M urea. In agreement with the mechanism of DNA local denaturation, we observe a sigmoid dependence of these effects on urea concentration. We find that the translocation times in urea are markedly slower than would be expected if the dynamics were governed primarily by viscous effects. Furthermore, we find that the sensitivity of the nanopore is sufficient to statistically differentiate between DNA molecules of nearly identical lengths differing only in sequence and AT content when placed in 3.5 M urea. Our results demonstrate that nanopores can detect subtle structural changes and are thus a valuable tool for detecting differences in biomolecules' environment.

Current oscillations generated by precipitate formation in the mixing zone between two solutions inside a nanopore

Unlike biological protein pores in lipid membranes, nanopores fabricated in synthetic materials can withstand a wide range of environmental conditions including the presence of organic solvents. This capability expands the potential of synthetic nanopores to monitor chemical reactions occurring at the interface between solutions of organic and aqueous character. In this work, nanopores fabricated in borosilicate glass or silicon nitride connected a predominantly organic solvent to an aqueous solvent, thereby generating a mixing zone between these solutions inside the pore. This configuration was exploited to precipitate small organic molecules with low aqueous solubility inside the nanopores, and concomitantly, to monitor this precipitation by the decrease of the ionic conductance through the nanopores over time. Hence, this method provides a means to induce and investigate the formation of nanoprecipitates or nanoparticles. Interestingly, precipitates with a slight electric charge were cleared from the pore, causing the conductance of the pore to return to its original value. This process repeated, resulting in stable oscillations of the ionic current. Although such oscillations might be useful in fluidic logic circuits, few conditions capable of generating oscillations in ionic currents have been reported. The frequency and amplitude of oscillations could be tuned by changing the concentration of the precipitating molecule, the pH of the electrolyte, and the applied potential bias. In addition to generating oscillations, nanopores that separate two different solutions may be useful for monitoring and mediating chemical reactions in the mixing zone between two solutions.

Photo-pens: a simple and versatile tool for maskless photolithography

We demonstrate conical pores etched in tracked glass chips for fabricating patterns at the micrometer scale. Highly fluorescent patterns based on photopolymerization of diacetylene films were formed by irradiating UV light through conical pores called "photo-pens". The properties of photopens were investigated through experiments, finite-difference-time-domain (FDTD) simulations and numerical calculations based on Fresnel equations. We show that the pattern dimensions are easily controlled by adjusting the exposure time. Thus, patterns with a range of dimensions can be fabricated without any need of changes in the pore diameter. Parallel patterning was also demonstrated by simultaneously exposing the films to photons through multiple pores in the chip. Our method provides an inexpensive, versatile, and efficient way for patterning without the use of sophisticated masks.

Large scale lithography-free nano channel array on polystyrene

This paper reports a new fabrication method of lithography-free nanochannel array. It is based on the cracking process on the surface of a polystyrene (PS) Petri-dish, one type of thermoplastic that is composed of uni-axial macromolecular chains. Under proper conditions, parallel nanochannels with equal interspaces are obtained. Control over the channel depth from 20 nm to 200 nm is achieved, with the channel length reaching tens of millimetres. The PDMS replication based on PS nanochannel array has been successfully carried out. In combination with the microstructure, both an ion enrichment device and a current rectification device are fabricated, and their quantified characters manifested the applicability of the channel array structure in nanofluidics.

Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors

Small RNA molecules have an important role in gene regulation and RNA silencing therapy, but it is challenging to detect these molecules without the use of time-consuming radioactive labelling assays or error-prone amplification methods. Here, we present a platform for the rapid electronic detection of probe-hybridized microRNAs from cellular RNA. In this platform, a target microRNA is first hybridized to a probe. This probe:microRNA duplex is then enriched through binding to the viral protein p19. Finally, the abundance of the duplex is quantified using a nanopore. Reducing the thickness of the membrane containing the nanopore to 6 nm leads to increased signal amplitudes from biomolecules, and reducing the diameter of the nanopore to 3 nm allows the detection and discrimination of small nucleic acids based on differences in their physical dimensions. We demonstrate the potential of this approach by detecting picogram levels of a liver-specific miRNA from rat liver RNA.

Fluxes of non-interacting and strongly repelling particles through a single conical channel: Analytical results and their numerical tests

Using a diffusion model of particle dynamics in the channel, we study entropic effects in channel-facilitated transport. We derive general expressions for the fluxes of non-interacting particles and particles that strongly repel each other through the channel of varying cross section area, assuming that the transport is driven by the difference in particle concentrations on the two sides of the membrane. For a special case of a right truncated cone expanding in the left-to-right direction, we show how the fluxes depend on the geometric parameters of the channel and on the particle concentrations. For non-interacting particles the flux is direction-independent in the sense that inversion of the concentration difference leads to the inversion of the direction of the flux without changing its magnitude. This symmetry is broken for repelling particles: The flux in the left-to-right direction exceeds its right-to-left counterpart. Our theoretical predictions are supported by three-dimensional Brownian dynamics simulations.

pH-tunable ion selectivity in carbon nanotube pores

The selectivity of ion transport in nanochannels is of primary importance for a number of physical, chemical, and biological processes ranging from fluid separation to ion-channel-regulated cellular processes. Fundamental understanding of these phenomena requires model nanochannels with well-defined and controllable structural properties. Carbon nanotubes provide an ideal choice for nanofluidic studies because of their simple chemistry and structure, the atomic scale smoothness and chemical inertness of the graphitic walls, and the tunability of their diameter and length. Here, we investigate the selectivity of single and, for the first time, binary salt mixtures transport through narrow carbon nanotubes that act as the only pores in a silicon nitride membrane. We demonstrate that negatively charged carboxylic groups are responsible for the ion rejection performance of carbon nanotube pores and that ion permeation of small salts can be tuned by varying solution pH. Investigation of the effect of solution composition and ion valences for binary electrolytes with common cation in a pressure-driven flow reveals that the addition of slower diffusing multivalent anions to a solution of faster diffusing monovalent anions favors permeation of the monovalent anion. Larger fractions and valences of the added multivalent anions lower the rejection of the monovalent anion. In some cases, we observe negative rejection at low monovalent ion content.

ATP-modulated ionic transport through synthetic nanochannels

Here, we demonstrate an anion controlled molecular gate based on synthetic ion channels modified with polyethyleneimine. For single conical nanochannels, addition of ATP leads to significant decrease in the rectified ion flux, representing the closure of the ionic gate. Complementary experiments performed with nanoporous membranes show that the flux of charged dye (NDS(2-)) through a cylindrical nanochannel array diminishes by the co-addition of ATP in the analyte solution.

Applications of biological pores in nanomedicine, sensing, and nanoelectronics

Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated - often regulated - functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics.

Fabrication of metallized nanopores in silicon nitride membranes for single-molecule sensing

The fabrication and characterization of a metallized nanopore structure for the sensing of single molecules is described. Pores of varying diameters (>10 nm) are patterned into free-standing silicon nitride membranes by electron-beam lithography and reactive ion etching. Structural characterization by transmission electron microscopy (TEM) and tomography reveals a conical pore shape with a 40 degrees aperture. Metal films of Ti/Au are vapor deposited and the pore shape and shrinking are studied as a function of evaporated film thickness. TEM tomography analysis confirms metalization of the inner pore walls as well as conservation of the conical pore shape. In electrical measurements of the transpore current in aqueous electrolyte solution, the pores feature very low noise. The applicability of the metallized pores for stochastic sensing is demonstrated in real-time translocation experiments of single lambda-DNA molecules. We observe exceptionally long-lasting current blockades with a fine structure of distinct current levels, suggesting an attractive interaction between the DNA and the PEGylated metallic pore walls.

Electrically facilitated translocations of proteins through silicon nitride nanopores: conjoint and competitive action of diffusion, electrophoresis, and electroosmosis

Solid-state nanopores bear great potential to be used to probe single proteins; however, the passage of proteins through nanopores was found to be complex, and unexpected translocation behavior with respect to the passage direction, rate, and duration was observed. Here we study the translocation of a model protein (avidin) through silicon nitride nanopores focusing on the electrokinetic effects that facilitate protein transport across the pore. The nanopore zeta potential zeta(pore) and the protein zeta potential zeta(protein) are measured independently as a function of solution pH. Our results reveal that electroosmotic transport may enhance or dominate and reverse electrophoretic transport in nanopores. The translocation behavior is rationalized by accounting for the charging states of the protein and the pore, respectively; the resulting translocation direction can be predicted according to the difference in zeta potentials, zeta(protein) - zeta(pore). When electrophoresis and electroosmosis cancel each other out, diffusion becomes an effective (and bias-independent) mechanism which facilitates protein transport across the pore at a significant rate.

Mapping the variation of the translocation α scaling exponent with nanopore width

The unbiased translocation of a coarse-grained polymer through a nanopore is investigated via Langevin dynamics simulations for polymers ranging from N=19 to 299 monomers in length and pore widths r p ranging from 1 to 10 times the monomer diameter. The exponent α derived from the scaling of the translocation time τ with respect to the molecular weight N is found to be heavily dependent on r p and increases from a value of 2.2 for r p=1.0 up to a saturation value of 3. The details of the translocation process also reveal that the average number of monomers in the pore [n p] not only varies as translocation proceeds but that for any polymer where the radius of gyration is greater than the radius of the available pore width, [n p] decreases with increasing N. Using these data to rescale the results according to a blob picture, the results retain sensitivity on the pore geometry as α varies from 2.2 to 2.65--a range which covers all results reported in previous studies.

Unraveling single-stranded DNA in a solid-state nanopore

Solid-state nanopores are an emerging class of single-molecule sensors. Whereas most studies so far focused on double-stranded DNA (dsDNA) molecules, exploration of single-stranded DNA (ssDNA) is of great interest as well, for example to employ such a nanopore device to read out the sequence. Here, we study the translocation of long random-sequence ssDNA through nanopores. Using atomic force microscopy, we observe the ssDNA to hybridize into a random coil, forming blobs of around 100 nm in diameter for 7 kb ssDNA. These large entangled structures have to unravel, when they arrive at the pore entrance. Indeed, we observe strong blockade events with a translocation time that is exponentially dependent on voltage, tau approximately e(-V/V(0)). Interestingly, this is very different than for dsDNA, for which tau approximately 1/V. We report translocations of ssDNA but also of ssDNA-dsDNA constructs where we compare the conductance-blockade levels for ssDNA versus dsDNA as a function of voltage.