Electrolytic transport through a synthetic nanometer-diameter pore

Amplification of single molecule translocation signal using β-strand peptide functionalized nanopores

Changes in ionic current flowing through nanopores due to binding or translocation of single biopolymer molecules enable their detection and characterization. It is, however, much more challenging to detect small molecules due to their rapid and small signal signature. Here we demonstrate the use of de novo designed peptides for functionalization of nanopores that enable the detection of a small analytes at the single molecule level. The detection relies on cooperative peptide conformational change that is induced by the binding of the small molecule to a receptor domain on the peptide. This change results in alteration of the nanopore effective diameter and hence induces current perturbation signal. On the basis of this approach, we demonstrate here the detection of diethyl 4-nitrophenyl phosphate (paraoxon), a poisonous organophosphate molecule. Paraoxon binding is induced by the incorporation of the catalytic triad of acetylcholine esterase in the hydrophilic domain of a short amphiphilic peptide and promotes β-sheet assembly of the peptide both in solution and for peptide molecules immobilized on solid surfaces. Nanopores coated with this peptide allowed the detection of paraoxon at the single molecule level revealing two binding arrangements. This unique approach, hence, provides the ability to study interactions of small molecules with the corresponding engineered receptors at the single molecule level. Furthermore, the suggested versatile platform may be used for the development of highly sensitive small analytes sensors.

Direct, concurrent measurements of the forces and currents affecting DNA in a nanopore with comparable topography

We report direct, concurrent measurements of the forces and currents associated with the translocation of a single-stranded DNA molecule tethered to the tip of an atomic force microscope (AFM) cantilever through synthetic pores with topagraphies comparable to the DNA. These measurements were performed to gauge the signal available for sequencing and the electric force required to impel a single molecule through synthetic nanopores ranging from 1.0 to 3.5 nm in diameter in silicon nitride membranes 6-10 nm thick. The measurements revealed that a molecule can slide relatively frictionlessly through a pore, but regular fluctuations are observed intermittently in the force (and the current) every 0.35-0.72 nm, which are attributed to individual nucleotides translating through the nanopore in a turnstile-like motion.

A mechanical nanogate based on a carbon nanotube for reversible control of ion conduction

Control of mass transport through nanochannels is of critical importance in many nanoscale devices and nanofiltration membranes. The gates in biological channels, which control the transport of substances across cell membranes, can provide inspiration for this purpose. Gates in many biological channels are formed by a constriction ringed with hydrophobic residues which can prevent ion conduction even when they are not completely physically occluded. In this work, we use molecular dynamics simulations to design a nanogate inspired by this hydrophobic gating mechanism. Deforming a carbon nanotube (12,12) with an external force can form a hydrophobic constriction in the centre of the tube that controls ion conduction. The simulation results show that increasing the magnitude of the applied force narrows the constriction and lowers the fluxes of K(+) and Cl(-) found under an electric field. With the exerted force larger than 5 nN, the constriction blocks the conduction of K(+) and Cl(-) due to partial dehydration while allowing for a noticeable water flux. Ion conduction can revert back to the unperturbed level upon force retraction, suggesting the reversibility of the nanogate. The force can be exerted by available experimental facilities, such as atomic force microscope (AFM) tips. It is found that partial dehydration in a continuous water-filled hydrophobic constriction is enough to close the channel, while full dewetting is not necessarily required. This mechanically deformed nanogate has many potential applications, such as a valve in nanofluidic systems to reversibly control ion conduction and a high-performance nanomachine for desalination and water treatment.

Single cell transfection with single molecule resolution using a synthetic nanopore

We report the development of a single cell gene delivery system based on electroporation using a synthetic nanopore, that is not only highly specific and very efficient but also transfects with single molecule resolution at low voltage (1 V) with minimal perturbation to the cell. Such a system can be used to control gene expression with unprecedented precision--no other method offers such capabilities.

Ionic permeability and mechanical properties of DNA origami nanoplates on solid-state nanopores

While DNA origami is a popular and versatile platform, its structural properties are still poorly understood. In this study we use solid-state nanopores to investigate the ionic permeability and mechanical properties of DNA origami nanoplates. DNA origami nanoplates of various designs are docked onto solid-state nanopores where we subsequently measure their ionic conductance. The ionic permeability is found to be high for all origami nanoplates. We observe the conductance of docked nanoplates, relative to the bare nanopore conductance, to increase as a function of pore diameter, as well as to increase upon lowering the ionic strength. The honeycomb lattice nanoplate is found to have slightly better overall performance over other plate designs. After docking, we often observe spontaneous discrete jumps in the current, a process which can be attributed to mechanical buckling. All nanoplates show a nonlinear current-voltage dependence with a lower conductance at higher applied voltages, which we attribute to a physical bending deformation of the nanoplates under the applied force. At sufficiently high voltage (force), the nanoplates are strongly deformed and can be pulled through the nanopore. These data show that DNA origami nanoplates are typically very permeable to ions and exhibit a number of unexpected mechanical properties, which are interesting in their own right, but also need to be considered in the future design of DNA origami nanostructures.

Biomimetic nanopore for sensitive and selective detection of Hg(ii) in conjunction with single-walled carbon nanotubes

Through SWNTs, duplex DNA derived from folding of single-stranded DNA can be quantitated with Zr⁴⁺–PEI coated cone-shaped nanopore. With Hg²⁺ detection, sensitivity and selectivity based on this paradigm is guaranteed without probe immobilization.

Accurate characterization of single track-etched, conical nanopores

Deviation from cone geometry significantly influences the ion current rectification through track-etched nanopores with tip radii smaller than 10 nm.

Uncertainty quantification in MD simulations of concentration driven ionic flow through a silica nanopore. I. Sensitivity to physical parameters of the pore

In this article, uncertainty quantification is applied to molecular dynamics (MD) simulations of concentration driven ionic flow through a silica nanopore. We consider a silica pore model connecting two reservoirs containing a solution of sodium (Na(+)) and chloride (Cl(-)) ions in water. An ad hoc concentration control algorithm is developed to simulate a concentration driven counter flow of ions through the pore, with the ionic flux being the main observable extracted from the MD system. We explore the sensitivity of the system to two physical parameters of the pore, namely, the pore diameter and the gating charge. First we conduct a quantitative analysis of the impact of the pore diameter on the ionic flux, and interpret the results in terms of the interplay between size effects and ion mobility. Second, we analyze the effect of gating charge by treating the charge density over the pore surface as an uncertain parameter in a forward propagation study. Polynomial chaos expansions and Bayesian inference are exploited to isolate the effect of intrinsic noise and quantify the impact of parametric uncertainty on the MD predictions. We highlight the challenges arising from the heterogeneous nature of the system, given the several components involved, and from the substantial effect of the intrinsic thermal noise.

Optoelectronic control of surface charge and translocation dynamics in solid-state nanopores

Nanopores can be used to detect and analyse biomolecules. However, controlling the translocation speed of molecules through a pore is difficult, which limits the wider application of these sensors. Here, we show that low-power visible light can be used to control surface charge in solid-state nanopores and can influence the translocation dynamics of DNA and proteins. We find that laser light precisely focused at a nanopore can induce reversible negative surface charge densities as high as 1 C m(-2), and that the effect is tunable on submillisecond timescales by adjusting the photon density. By modulating the surface charge, we can control the amount of electroosmotic flow through the nanopore, which affects the speed of translocating biomolecules. In particular, a few milliwatts of green light can reduce the translocation speed of double-stranded DNA by more than an order of magnitude and the translocation speed of small globular proteins such as ubiquitin by more than two orders of magnitude. The laser light can also be used to unclog blocked pores. Finally, we discuss a mechanism to account for the observed optoelectronic phenomenon.

Differentiation of short, single-stranded DNA homopolymers in solid-state nanopores

In the last two decades, new techniques that monitor ionic current modulations as single molecules pass through a nanoscale pore have enabled numerous single-molecule studies. While biological nanopores have recently shown the ability to resolve single nucleotides within individual DNA molecules, similar developments with solid-state nanopores have lagged, due to challenges both in fabricating stable nanopores of similar dimensions as biological nanopores and in achieving sufficiently low-noise and high-bandwidth recordings. Here we show that small silicon nitride nanopores (0.8- to 2-nm diameter in 5- to 8-nm-thick membranes) can resolve differences between ionic current signals produced by short (30 base) ssDNA homopolymers (poly(dA), poly(dC), poly(dT)), when combined with measurement electronics that allow a signal-to-noise ratio of better than 10 to be achieved at 1-MHz bandwidth. While identifying intramolecular DNA sequences with silicon nitride nanopores will require further improvements in nanopore sensitivity and noise levels, homopolymer differentiation represents an important milestone in the development of solid-state nanopores.

Direct visualization of single-molecule translocations through synthetic nanopores comparable in size to a molecule

A nanopore is the ultimate analytical tool. It can be used to detect DNA, RNA, oligonucleotides, and proteins with submolecular sensitivity. This extreme sensitivity is derived from the electric signal associated with the occlusion that develops during the translocation of the analyte across a membrane through a pore immersed in electrolyte. A larger occluded volume results in an improvement in the signal-to-noise ratio, and so the pore geometry should be made comparable to the size of the target molecule. However, the pore geometry also affects the electric field, the charge density, the electro-osmotic flow, the capture volume, and the response time. Seeking an optimal pore geometry, we tracked the molecular motion in three dimensions with high resolution, visualizing with confocal microscopy the fluorescence associated with DNA translocating through nanopores with diameters comparable to the double helix, while simultaneously measuring the pore current. Measurements reveal single molecules translocating across the membrane through the pore commensurate with the observation of a current blockade. To explain the motion of the molecule near the pore, finite-element simulations were employed that account for diffusion, electrophoresis, and the electro-osmotic flow. According to this analysis, detection using a nanopore comparable in diameter to the double helix represents a compromise between sensitivity, capture volume, the minimum detectable concentration, and response time.

Voltage-driven transport of ions and DNA through nanocapillaries

We study the effect of salt concentration on the ionic conductance and translocation of single DNA molecules through nanocapillaries made out of quartz glass. DNA translocation experiments were performed in aqueous solution for concentrations of KCl between 10 mM and 2 M while ion conductance was characterized from 1 mM to 2 M KCl concentration. Here, we develop a model for the conductance of conical nanocapillaries taking into consideration the surface charge of the quartz glass. We demonstrate that the conductance of our nanocapillaries shows similar behavior to silicon oxide nanopores at low and high KCl concentrations. Finally, we show that DNA translocations in high KCl concentrations (400 mM-2 M) cause a reduction in the ionic current. In contrast, DNA translocations at low KCl concentrations (10-300 mM) lead to increases in the ionic current. Our new results, which until now have not been shown for nanocapillaries, can be well understood with an adapted model.

Conductance-Based Determination of Solid-State Nanopore Size and Shape: An Exploration of Performance Limits

Knowledge of nanopore size and shape is critical for many implementations of these single-molecule sensing elements. Geometry determination by fitting the electrolyte-concentration-dependence of the conductance of surface-charged, solid-state nanopores has been proposed to replace demanding electron microscope-based methods. The functional form of the conductance poses challenges for this method by restricting the number of free parameters used to characterize the nanopore. We calculated the electrolyte-dependent conductance of nanopores with an exponential-cylindrical radial profile using three free geometric parameters; this profile, itself, could not be uniquely geometry-optimized by the conductance. Several different structurally simplified models, however, generated quantitative agreement with the conductance, but with errors exceeding 40% for estimates of key geometrical parameters. A tractable conical-cylindrical model afforded a good characterization of the nanopore size and shape, with errors of less than 1% for the limiting radius. Understanding these performance limits provides a basis for using and extending analytical nanopore conductance models.

Large apparent electric size of solid-state nanopores due to spatially extended surface conduction

Ion transport through nanopores drilled in thin membranes is central to numerous applications, including biosensing and ion selective membranes. This paper reports experiments, numerical calculations, and theoretical predictions demonstrating an unexpectedly large ionic conduction in solid-state nanopores, taking its origin in anomalous entrance effects. In contrast to naive expectations based on analogies with electric circuits, the surface conductance inside the nanopore is shown to perturb the three-dimensional electric current streamlines far outside the nanopore in order to meet charge conservation at the pore entrance. This unexpected contribution to the ionic conductance can be interpreted in terms of an apparent electric size of the solid-state nanopore, which is much larger than its geometric counterpart whenever the number of charges carried by the nanopore surface exceeds its bulk counterpart. This apparent electric size, which can reach hundreds of nanometers, can have a major impact on the electrical detection of translocation events through nanopores, as well as for ionic transport in biological nanopores.

Protein transport through a narrow solid-state nanopore at high voltage: experiments and theory

We report experimentally the transport of an unfolded protein through a narrow solid-state nanopore of 3 nm diameter as a function of applied voltage. The random coil polypeptide chain is larger than the nanopore. The event frequency dependency of current blockades from 200 to 750 mV follows a van't Hoff-Arrhenius law due to the confinement of the unfolded chain. The protein is an extended conformation inside the pore at high voltage. We observe that the protein dwell time decreases exponentially at medium voltage and is inversely proportional to voltage for higher values. This is consistent with the translocation mechanism where the protein is confined in the pore, creating an entropic barrier, followed by electrophoretic transport. We compare these results to our previous work with a larger pore of 20 nm diameter. Our data suggest that electro-osmotic flow and protein adsorption on the narrowest nanopore wall are minimized. We discuss the experimental data obtained as compared with recent theory for the polyelectrolyte translocation process. This theory reproduces clearly the experimental crossover between the entropic barrier regime with medium voltage and the electrophoretic regime with higher voltage.

Using a nanopore for single molecule detection and single cell transfection

We assert that it is possible to trap and identify proteins, and even (conceivably) manipulate proteins secreted from a single cell (i.e. the secretome) through transfection via electroporation by exploiting the exquisite control over the electrostatic potential available in a nanopore. These capabilities may be leveraged for single cell analysis and transfection with single molecule resolution, ultimately enabling a careful scrutiny of tissue heterogeneity.

Resistive-pulse detection of multilamellar liposomes

The resistive-pulse method was used to monitor the pressure-driven translocation of multilamellar liposomes with radii between 190 and 450 nm through a single conical nanopore embedded in a glass membrane. Liposomes (0% and 5% 1,2-dioleoyl-sn-glycero-3-phospho-l-serine (sodium salt) in 1,2-dilauroyl-sn-glycero-3-phosphocholine or 0%, 5%, and 9% 1,2-dipalmitoyl-sn-glycero-3-phospho(1'-rac-glycerol) (sodium salt) in 1,2-dipalmitoyl-sn-glycero-3-phosphocholine) were prepared by extrusion through a polycarbonate membrane. Liposome translocation through a glass nanopore was studied as a function of nanopore size and the temperature relative to the lipid bilayer transition temperature, T(c). All translocation events through pores larger than the liposome, regardless of temperature, show translocation times between 30 and 300 μs and current pulse heights between 0.2% and 15% from the open pore baseline. However, liposomes at temperatures below the T(c) were captured at the pore orifice when translocation was attempted through pores of smaller dimensions, but squeezed through the same pores when the temperature was raised above T(c). The results provide insights into the deformation and translocation of individual liposomes through a porous material.

Direct observation of stick-slip movements of water nanodroplets induced by an electron beam

Dynamics of the first few nanometers of water at the interface are encountered in a wide range of physical, chemical, and biological phenomena. A simple but critical question is whether interfacial forces at these nanoscale dimensions affect an externally induced movement of a water droplet on a surface. At the bulk-scale water droplets spread on a hydrophilic surface and slip on a nonwetting, hydrophobic surface. Here we report the experimental description of the electron beam-induced dynamics of nanoscale water droplets by direct imaging the translocation of 10- to 80-nm-diameter water nanodroplets by transmission electron microscopy. These nanodroplets move on a hydrophilic surface not by a smooth flow but by a series of stick-slip steps. We observe that each step is preceded by a unique characteristic deformation of the nanodroplet into a toroidal shape induced by the electron beam. We propose that this beam-induced change in shape increases the surface free energy of the nanodroplet that drives its transition from stick to slip state.

How to understand and interpret current flow in nanopore/electrode devices

Nanopore-based single-molecule sensors have become an important class of analytical devices that have in some cases already reached the market place. Traditionally operated in a two-electrode configuration, devices with three or more electrodes have emerged recently, for example with a view on switching the transport properties of the nanopore or even tunneling-based detection of analytes with the ultimate goal of inexpensive and ultrafast DNA sequencing. How do these additional electrodes affect the current distribution in the cell and hence the sensor performance? This is significantly less clear and thus in focus here. We use impedance modeling of a prototypical three-electrode nanopore sensor and show that, depending on the conditions, standard experimental device characterization is severely affected by the presence of the third electrode. On the other hand, the simulations also provide guidelines on how to avoid such complications, identify "safe" operating conditions, and design criteria for optimized nanopore sensors.

Coarse-grained molecular dynamics simulation of DNA translocation in chemically modified nanopores

Solid-state nanopores provide a direct means to detect and analyze DNA and proteins. In a typical setup, the DNA molecules travel through a nanopore under electrophoretic voltage bias. The nanopore is sandwiched between two chambers that are filled with ionic solution. A major challenge in using solid-state nanopores for DNA sequencing and gene detection is to improve their selectivity and detection sensitivity. To achieve these goals, one solution is to functionalize the nanopores by chemically modifying the pore walls with silanes or nucleic acids. However, little is known about molecular interactions in functionalized nanopores. This paper presents DNA translocation dynamics and the mechanism of DNA sequencing in a functionalized nanopore through a coarse-grained molecular dynamics model. The DNA nucleotide is coarse-grained into two interaction sites: one site corresponds to the base group and the other encompasses the phosphate and sugar groups. The water molecules are included in the model implicitly through Langevin dynamics. The coarse-grained model immensely improves the computational efficiency while still capturing the essential translocation dynamics. The model characterizes important physical properties of functionalized nanopores such as the effective pore diameter and effect of biasing voltage on the DNA translocation dynamics. The model reveals a nonlinear relationship between translocation speed of DNA and applied voltage. Moreover, DNA translocation in nanopores functionalized with hairpin-loop (HPL) DNA and single-stranded DNA (ss-DNA) shows significant differences: a target DNA is found to translocate through a ss-DNA coated nanopore 9 times faster than through an HPL coated one at a bias of 100 mV, putatively from lower stiffness of ss-DNA than that for HPL. The DNA translocation speed is also largely influenced by interaction potential between the DNA and surface-tethered molecules. The results reveal that such selective translocation, distinctly different translocation dynamics of target DNA molecules largely stem from the flexibility and orientation of the surface-tethered molecules. These findings can significantly impact the rational design of DNA transport experiments leading to rapid molecule-level diagnostics.

Rectification of the current in alpha-hemolysin pore depends on the cation type: the alkali series probed by MD simulations and experiments

A striking feature of the alpha-hemolysin channel-a prime candidate for biotechnological applications-is the dependence of its ionic conductance on the magnitude and direction of the applied bias. Through a combination of lipid bilayer single-channel recording and molecular dynamics (MD) simulations, we characterized the current-voltage relationship of alpha-hemolysin for all alkali chloride salts at neutral pH. The rectification of the ionic current was found to depend on the type of cations and increase from Li(+) to Cs(+). Analysis of the MD trajectories yielded a simple quantitative model that related the ionic current to the electrostatic potential, the concentration and effective mobility of ions in the channel. MD simulations reveal that the major contribution to the current asymmetry and rectification properties originates from the cationic contribution to the current that is significantly reduced in a cationic dependent way when the membrane polarity is reversed. The variation of chloride current was found to be less important. We report that the differential affinity of cations for the charged residues positioned at the channel's end modulates the number of ions inside the channel stem thus affecting the current properties. Through direct comparison of simulation and experiment, this study evaluates the accuracy of the MD method for prediction of the asymmetric, voltage dependent conductances of a membrane channel.

Modeling nanopores for sequencing DNA

Using nanopores to sequence DNA rapidly and at a low cost has the potential to radically transform the field of genomic research. However, despite all the exciting developments in the field, sequencing DNA using a nanopore has yet to be demonstrated. Among the many problems that hinder development of the nanopore sequencing methods is the inability of current experimental techniques to visualize DNA conformations in a nanopore and directly relate the microscopic state of the system to the measured signal. We have recently shown that such tasks could be accomplished through computation. This chapter provides step-by-step instructions of how to build atomic scale models of biological and solid-state nanopore systems, use the molecular dynamics method to simulate the electric field-driven transport of ions and DNA through the nanopores, and analyze the results of such computational experiments.

Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix

It is now possible to slow and trap a single molecule of double-stranded DNA (dsDNA), by stretching it using a nanopore, smaller in diameter than the double helix, in a solid-state membrane. By applying an electric force larger than the threshold for stretching, dsDNA can be impelled through the pore. Once a current blockade associated with a translocating molecule is detected, the electric field in the pore is switched in an interval less than the translocation time to a value below the threshold for stretching. According to molecular dynamics (MD) simulations, this leaves the dsDNA stretched in the pore constriction with the base-pairs tilted, while the B-form canonical structure is preserved outside the pore. In this configuration, the translocation velocity is substantially reduced from 1 bp/10 ns to approximately 1 bp/2 ms in the extreme, potentially facilitating high fidelity reads for sequencing, precise sorting, and high resolution (force) spectroscopy.

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.

Computational microscopy of the role of protonable surface residues in nanoprecipitation oscillations

A novel phenomenon has recently been reported in polymeric nanopores. This phenomenon, so-called nanoprecipitation, is characterized by the transient formation of precipitates in the nanopore lumen, producing a sequence of low and high conductance states in the ionic current through the pore. By means of all-atom molecular dynamics simulations, we studied nanoprecipitation for polyethylene terephthalate nanopore immersed in electrolytic solution containing calcium phosphate, covering a total simulation time of 1.24 micros. Our results suggest that protonable surface residues at the nanopore surface, namely carboxyl groups, trigger the formation of precipitates that strongly adhere to the surface, blocking the pore and producing the low conductance state. On the basis of the simulations, we propose a mechanism for the formation of the high conductance state; the mechanism involves detachment of the precipitate from the surface due to reprotonation of carboxyl groups and subsequent translocation of the precipitate out of the pore.

DNA translocation through an array of kinked nanopores

Synthetic solid-state nanopores are being intensively investigated as single-molecule sensors for detection and characterization of DNA, RNA and proteins. This field has been inspired by the exquisite selectivity and flux demonstrated by natural biological channels and the dream of emulating these behaviours in more robust synthetic materials that are more readily integrated into practical devices. So far, the guided etching of polymer films, focused ion-beam sculpting, and electron-beam lithography and tuning of silicon nitride membranes have emerged as three promising approaches to define synthetic solid-state pores with sub-nanometre resolution. These procedures have in common the formation of nominally cylindrical or conical pores aligned normal to the membrane surface. Here we report the formation of 'kinked' silica nanopores, using evaporation-induced self-assembly, and their further tuning and chemical derivatization using atomic-layer deposition. Compared with 'straight through' proteinaceous nanopores of comparable dimensions, kinked nanopores exhibit up to fivefold reduction in translocation velocity, which has been identified as one of the critical issues in DNA sequencing. Additionally, we demonstrate an efficient two-step approach to create a nanopore array exhibiting nearly perfect selectivity for ssDNA over dsDNA. We show that a coarse-grained drift-diffusion theory with a sawtooth-like potential can reasonably describe the velocity and translocation time of DNA through the pore. By control of pore size, length and shape, we capture the main functional behaviours of protein pores in our solid-state nanopore system.

Molecular diagnostics for personal medicine using a nanopore

Semiconductor nanotechnology has created the ultimate analytical tool: a nanopore with single molecule sensitivity. This tool offers the intriguing possibility of high-throughput, low cost sequencing of DNA with the absolute minimum of material and preprocessing. The exquisite single molecule sensitivity obviates the need for costly and error-prone procedures like polymerase chain reaction amplification. Instead, nanopore sequencing relies on the electric signal that develops when a DNA molecule translocates through a pore in a membrane. If each base pair has a characteristic electrical signature, then ostensibly a pore could be used to analyze the sequence by reporting all of the signatures in a single read without resorting to multiple DNA copies. The potential for a long read length combined with high translocation velocity should make resequencing inexpensive and allow for haplotyping and methylation profiling in a chromosome.

Characterizing the surface charge of synthetic nanomembranes by the streaming potential method

The inference of the surface charge of polyethylene glycol (PEG)-coated and uncoated silicon membranes with nanoscale pore sizes from streaming potential measurements in the presence of finite electric double layer (EDL) effects is studied theoretically and experimentally. The developed theoretical model for inferring the pore wall surface charge density from streaming potential measurements is applicable to arbitrary pore cross-sectional shapes and accounts for the effect of finite salt concentration on the ionic mobilities and the thickness of the deposited layer of PEG. Theoretical interpretation of the streaming potential data collected from silicon membranes having nanoscale pore sizes, with/without pore wall surface modification with PEG, indicates that finite electric double layer (EDL) effects in the pore-confined electrolyte significantly affect the interpretation of the membrane charge and that surface modification with PEG leads to a reduction in the pore wall surface charge density. The theoretical model is also used to study the relative significance of the following uniquely nanoscale factors affecting the interpretation of streaming potential in moderate to strongly charged pores: altered net charge convection by applied pressure differentials, surface-charge effects on ionic conduction, and electroosmotic convection of charges.

Probing single nanometer-scale pores with polymeric molecular rulers

We previously demonstrated that individual molecules of single-stranded DNA can be driven electrophoretically through a single Staphylococcus aureus alpha-hemolysin ion channel. Polynucleotides thread through the channel as extended chains and the polymer-induced ionic current blockades exhibit stable modes during the interactions. We show here that polynucleotides can be used to probe structural features of the alpha-hemolysin channel itself. Specifically, both the pore length and channel aperture profile can be estimated. The results are consistent with the channel crystal structure and suggest that polymer-based "molecular rulers" may prove useful in deducing the structures of nanometer-scale pores in general.

Deciphering ionic current signatures of DNA transport through a nanopore

Within just a decade from the pioneering work demonstrating the utility of nanopores for molecular sensing, nanopores have emerged as versatile systems for single-molecule manipulation and analysis. In a typical setup, a gradient of the electrostatic potential captures charged solutes from the solution and forces them to move through a single nanopore, across an otherwise impermeable membrane. The ionic current blockades resulting from the presence of a solute in a nanopore can reveal the type of the solute, for example, the nucleotide makeup of a DNA strand. Despite great success, the microscopic mechanisms underlying the functionality of such stochastic sensors remain largely unknown, as it is not currently possible to characterize the microscopic conformations of single biomolecules directly in a nanopore and thereby unequivocally establish the causal relationship between the observables and the microscopic events. Such a relationship can be determined using molecular dynamics-a computational method that can accurately predict the time evolution of a molecular system starting from a given microscopic state. This article describes recent applications of this method to the process of DNA transport through biological and synthetic nanopores.

Aptamer-encoded nanopore for ultrasensitive detection of bioterrorist agent ricin at single-molecule resolution

The molecular-scale pore structure, called nanopore, can be formed from protein ion channels by genetic engineering or fabricated on solid substrates using fashion nanotechnology. Target molecules in interaction with the functionalized lumen of nanopore, can produce characteristic changes in the pore conductance, which act as fingerprints, allowing us to identify single molecules and simultaneously quantify each target species in the mixture. Nanopore sensors have been created for tremendous biomedical detections, with targets ranging from metal ions, drug compounds and cellular second messengers, to proteins and DNAs. Here we will review our recent discoveries with a lab-in-hand glass nanopore: single-molecule discrimination of chiral enantiomers with a trapped cyclodextrin, and sensing of bioterrorist agent ricin.

Nanopores in solid-state membranes engineered for single molecule detection

A nanopore is an analytical tool with single molecule sensitivity. For detection, a nanopore relies on the electrical signal that develops when a molecule translocates through it. However, the detection sensitivity can be adversely affected by noise and the frequency response. Here, we report measurements of the frequency and noise performance of nanopores </=8 nm in diameter in membranes compatible with semiconductor processing. We find that both the high frequency and noise performance are compromised by parasitic capacitances. From the frequency response we extract the parameters of lumped element models motivated by the physical structure that elucidates the parasitics, and then we explore four strategies for improving the electrical performance. We reduce the parasitic membrane capacitances using: (1) thick Si(3)N(4) membranes; (2) miniaturized composite membranes consisting of Si(3)N(4) and polyimide; (3) miniaturized membranes formed from metal-oxide-semiconductor (MOS) capacitors; and (4) capacitance compensation through external circuitry, which has been used successfully for patch clamping. While capacitance compensation provides a vast improvement in the high frequency performance, mitigation of the parasitic capacitance through miniaturization offers the most promising route to high fidelity electrical discrimination of single molecules.

Single molecule sensing by nanopores and nanopore devices

Molecular-scale pore structures, called nanopores, can be assembled by protein ion channels through genetic engineering or be artificially fabricated on solid substrates using fashion nanotechnology. When target molecules interact with the functionalized lumen of a nanopore, they characteristically block the ion pathway. The resulting conductance changes allow for identification of single molecules and quantification of target species in the mixture. In this review, we first overview nanopore-based sensory techniques that have been created for the detection of myriad biomedical targets, from metal ions, drug compounds, and cellular second messengers to proteins and DNA. Then we introduce our recent discoveries in nanopore single molecule detection: (1) using the protein nanopore to study folding/unfolding of the G-quadruplex aptamer; (2) creating a portable and durable biochip that is integrated with a single-protein pore sensor (this chip is compared with recently developed protein pore sensors based on stabilized bilayers on glass nanopore membranes and droplet interface bilayer); and (3) creating a glass nanopore-terminated probe for single-molecule DNA detection, chiral enantiomer discrimination, and identification of the bioterrorist agent ricin with an aptamer-encoded nanopore.

Ionic current flow through ZnO nanotubes

The control of ionic current (electrolyte) flow through zinc oxide (ZnO) nanotubes is investigated. We studied a structure operating like a field effect transistor with a tunable ionic flow. The main investigation tool used was molecular dynamics simulation. We complemented the molecular dynamics simulation with the site binding method in order to study the effect of the double layer on the ionic current flowing through the nanotube. We achieved this by considering the electrolyte solution as a virtual semiconductor wire. The double layer capacitance and surface charge of the inner walls of the ZnO nanotube have been calculated. The results indicate that ZnO nanotubes can be tuned to operate as ion selectors. ZnO nanotubes exhibit enhanced functionality with characteristics similar to those of the nanopore membrane.

Quantized ionic conductance in nanopores

Ionic transport in nanopores is a fundamentally and technologically important problem in view of its occurrence in biological processes and its impact on novel DNA sequencing applications. Using molecular dynamics simulations we show that ion transport may exhibit strong nonlinearities as a function of the pore radius reminiscent of the conductance quantization steps as a function of the transverse cross section of quantum point contacts. In the present case, however, conductance steps originate from the break up of the hydration layers that form around ions in aqueous solution. We discuss this phenomenon and the conditions under which it should be experimentally observable.

Capturing single molecules of immunoglobulin and ricin with an aptamer-encoded glass nanopore

Nanopore-based single-molecule biosensors have been extensively studied. Protein pores that have receptors attached to them are target-selective, but their real-time applications are limited by the fragility of the lipid membrane into which the protein pores are embedded. Synthetic nanopores are more stable and provide flexible pore sizes, but the selectivity is low when detecting in the translocation mode. In spite of modifications with probing molecules, such as antibodies, to potentiate specific targeting, these nanopores fail to bind individual target molecules. Distinguishing between binding and translocation blocks remains unsolved. Here, we propose an aptamer-encoded nanopore that overcomes these challenges. Aptamers are well-known probing oligonucleotides that have high sensitivity and selectivity. In contrast to antibodies, aptamers are much smaller than their targets, rendering target blockades in the nanopore much more distinguishable. We used aptamer-encoded nanopores to detect single molecules of immunoglobulin E and the bioterrorist agent ricin, sequentially captured by the immobilized aptamer in the sensing zone of the pore. The functional nanopore also probed sequence-dependent aptamer-protein interactions. These findings will facilitate the development of a universal nanopore for multitarget detection.

Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore

Restriction endonucleases are used prevalently in recombinant DNA technology because they bind so stably to a specific target sequence and, in the presence of cofactors, cleave double-helical DNA specifically at a target sequence at a high rate. Using synthetic nanopores along with molecular dynamics (MD), we have analyzed with atomic resolution how a prototypical restriction endonuclease, EcoRI, binds to the DNA target sequence--GAATTC--in the absence of a Mg(2+) ion cofactor. We have previously shown that there is a voltage threshold for permeation of DNA bound to restriction enzymes through a nanopore that is associated with a nanonewton force required to rupture the complex. By introducing mutations in the DNA, we now show that this threshold depends on the recognition sequence and scales linearly with the dissociation energy, independent of the pore geometry. To predict the effect of mutation in a base pair on the free energy of dissociation, MD is used to qualitatively rank the stability of bonds in the EcoRI-DNA complex. We find that the second base in the target sequence exhibits the strongest binding to the protein, followed by the third and first bases, with even the flanking sequence affecting the binding, corroborating our experiments.

Synthetic proton-gated ion channels via single solid-state nanochannels modified with responsive polymer brushes

The creation of switchable and tunable nanodevices displaying transport properties similar to those observed in biological pores poses a major challenge in molecular nanotechnology. Here, we describe the construction of a fully "abiotic" nanodevice whose transport properties can be accurately controlled by manipulating the proton concentration in the surrounding environment. The ionic current switching characteristics displayed by the nanochannels resemble the typical behavior observed in many biological channels that fulfill key pH-dependent transport functions in living organisms, that is, the nanochannel can be switched from an "off" state to an "on" state in response to a pH drop. The construction of such a chemical nanoarchitecture required the integration of stable and ductile macromolecular building blocks constituted of pH-responsive poly(4-vinyl pyridine) brushes into solid state nanopores that could act as gate-keepers managing and constraining the flow of ionic species through the confined environment. In this context, we envision that the integration of environmental stimuli-responsive brushes into solid-state nanochannels would provide a plethora of new chemical alternatives for molecularly design robust signal-responsive "abiotic" devices mimicking the function of proton-gated ion channels commonly encountered in biological membranes.

Reverse DNA translocation through a solid-state nanopore by magnetic tweezers

Voltage-driven DNA translocation through nanopores has attracted wide interest for many potential applications in molecular biology and biotechnology. However, it is intrinsically difficult to control the DNA motion in standard DNA translocation processes in which a strong electric field is required in drawing DNA into the pore, but it also leads to uncontrollable fast DNA translocation. Here we explore a new type of DNA translocation. We dub it 'reverse DNA translocation', in which the DNA is pulled through a nanopore mechanically by a magnetic bead, driven by a magnetic-field gradient. This technique is compatible with simultaneous ionic current measurements and is suitable for multiple nanopores, paving the way for large scale applications. We report the first experiment of reverse DNA translocation through a solid-state nanopore using magnetic tweezers.