Ion-beam sculpting at nanometre length scales

Aviram-Ratner rectifying mechanism for DNA base-pair sequencing through graphene nanogaps

We demonstrate that biological molecules such as Watson-Crick DNA base pairs can behave as biological Aviram-Ratner electrical rectifiers because of the spatial separation and weak hydrogen bonding between the nucleobases. We have performed a parallel computational implementation of the ab initio non-equilibrium Green's function (NEGF) theory to determine the electrical response of graphene--base-pair--graphene junctions. The results show an asymmetric (rectifying) current-voltage response for the cytosine-guanine base pair adsorbed on a graphene nanogap. In sharp contrast we find a symmetric response for the thymine-adenine case. We propose applying the asymmetry of the current-voltage response as a sensing criterion to the technological challenge of rapid DNA sequencing via graphene nanogaps.

Atom-by-atom nucleation and growth of graphene nanopores

Graphene is an ideal thin membrane substrate for creating molecule-scale devices. Here we demonstrate a scalable method for creating extremely small structures in graphene with atomic precision. It consists of inducing defect nucleation centers with energetic ions, followed by edge-selective electron recoil sputtering. As a first application, we create graphene nanopores with radii as small as 3 Å, which corresponds to 10 atoms removed. We observe carbon atom removal from the nanopore edge in situ using an aberration-corrected electron microscope, measure the cross-section for the process, and obtain a mean edge atom displacement energy of 14.1 ± 0.1 eV. This approach does not require focused beams and allows scalable production of single nanopores and arrays of monodisperse nanopores for atomic-scale selectively permeable membranes.

Engineering of micro- and nanostructured surfaces with anisotropic geometries and properties

Widespread approaches to fabricate surfaces with robust micro- and nanostructured topographies have been stimulated by opportunities to enhance interface performance by combining physical and chemical effects. In particular, arrays of asymmetric surface features, such as arrays of grooves, inclined pillars, and helical protrusions, have been shown to impart unique anisotropy in properties including wetting, adhesion, thermal and/or electrical conductivity, optical activity, and capability to direct cell growth. These properties are of wide interest for applications including energy conversion, microelectronics, chemical and biological sensing, and bioengineering. However, fabrication of asymmetric surface features often pushes the limits of traditional etching and deposition techniques, making it challenging to produce the desired surfaces in a scalable and cost-effective manner. We review and classify approaches to fabricate arrays of asymmetric 2D and 3D surface features, in polymers, metals, and ceramics. Analytical and empirical relationships among geometries, materials, and surface properties are discussed, especially in the context of the applications mentioned above. Further, opportunities for new fabrication methods that combine lithography with principles of self-assembly are identified, aiming to establish design principles for fabrication of arbitrary 3D surface textures over large areas.

Reliable fabrication of 3 nm gaps between nanoelectrodes by electron-beam lithography

The reliable fabrication of nanoelectrode pairs with predefined separations in the few nanometer range is an essential prerequisite for future nanoelectronic devices. Here we demonstrate a fine-tuned electron-beam lithographic (EBL) fabrication route which is suitable for defining nanoelectrode pairs with a gap size down to 3 ± 1 nm and with a yield of 55%. This achievement is based on an optimized two-layer resist system in combination with an adopted developer system, as well as on an elaborated nanoelectrode pattern design taking into consideration the EBL inherent proximity effect. Thus, even a structural control in the nanometer scale is achieved in the EBL process.

Nanopore detection of single molecule RNAP-DNA transcription complex

In the past decade, a number of single-molecule methods have been developed with the aim of investigating single protein and nucleic acid interactions. For the first time we use solid-state nanopore sensing to detect a single E. coli RNAP-DNA transcription complex and single E. coli RNAP enzyme. On the basis of their specific conductance translocation signature, we can discriminate and identify between those two types of molecular translocations and translocations of bare DNA. This opens up a new perspectives for investigating transcription processes at the single-molecule level.

Size evolution and surface characterization of solid-state nanopores in different aqueous solutions

The stability and surface evolution of solid-state nanopores in aqueous solutions are extremely important since they would get immersed in solutions during DNA translocation experiment for DNA analyses. In this work, we systematically studied the size evolution of SiN nanopores in ethanol, deionized water and potassium chloride (KCl) solutions by careful surface characterization and composition analyses using a transmission electron microscope. Surprisingly, we found that nanopores closed up completely in ethanol in an hour and showed a 30% and 20% size decrease in deionized water and KCl solutions, respectively. Strong evidence of surface oxidation was found by composition analyses in the nanopore area. Nanopore size evolution was strongly dependent on initial pore size and solution pH value. In pH = 13 KCl solution, SiN nanopores were observed to increase in size instead of decrease. The results not only provide useful information for DNA detection based on solid-state nanopores, but can also guide design and application of other nanodevices exposed to electrolyte-solvent systems such as cell-on-a-chip devices and biosensors.

Diffusional motion of a particle translocating through a nanopore

The influence of diffusional motion on the capture and release of individual nanoparticles as they are driven through a conical-shaped glass nanopore membrane (GNM) by pressure-induced flow is reported. In these experiments, one to several hundred particles are driven through the orifice of the nanopore. Following the initial translocation, the pressure is reversed and the particles are driven through the GNM orifice in the reverse direction. The resistive-pulse technique is used to monitor the temporal sequence of particle capture and release translocations. The size of the particles (120-160 nm) and the direction of translocation can be determined from the pulse amplitude and shape. The stochastic influence of diffusion on particle trajectories has been investigated, including instantaneous transfer rate, release probability, and cumulative release success rate. We demonstrate that the sequence of particle translocations in the capture step (a, b, c... where the letters represent different particles) is largely preserved and can be read out by resistive-pulse signature during the release translocations (...c, b, a). The observed stochastic events are in good agreement with a convective diffusion model of particle trajectory within the confined geometry of the nanopore. The pressure-reversal technique opens new avenues for chemical analysis of particles using resistive-pulse methods.

Nanopatterning on nonplanar and fragile substrates with ice resists

Electron beam (e-beam) lithography using polymer resists is an important technology that provides the spatial resolution needed for nanodevice fabrication. But it is often desirable to pattern nonplanar structures on which polymeric resists cannot be reliably applied. Furthermore, fragile substrates, such as free-standing nanotubes or thin films, cannot tolerate the vigorous mechanical scrubbing procedures required to remove all residual traces of the polymer resist. Here we demonstrate several examples where e-beam lithography using an amorphous ice resist eliminates both of these difficulties and enables the fabrication of unique nanoscale device structures in a process we call ice lithography. (1, 2) We demonstrate the fabrication of micro- and nanostructures on the tip of atomic force microscope probes, microcantilevers, transmission electron microscopy grids, and suspended single-walled carbon nanotubes. Our results show that by using amorphous water ice as an e-beam resist, a new generation of nanodevice structures can be fabricated on nonplanar or fragile substrates.

Probing Access Resistance of Solid-state Nanopores with a Scanning Probe Microscope Tip

An apparatus that integrates solid-state nanopore ionic current measurement with a Scanning Probe Microscope has been developed. When a micrometer-scale scanning probe tip is near a voltage biased nanometer-scale pore (10-100 nm), the tip partially blocks the flow of ions to the pore and increases the pore access resistance. The apparatus records the current blockage caused by the probe tip and the location of the tip simultaneously. By measuring the current blockage map near a nanopore as a function of the tip position in 3D space in salt solution, we estimate the relative pore resistance increase due to the tip, ΔR/R(0), as a function of the tip location, nanopore geometry, and salt concentration. The amplitude of ΔR/R(0) also depends on the ratio of the pore length to its radius as Ohm's law predicts. When the tip is very close to the pore surface, ~10 nm, our experiments show that ΔR/R(0) depends on salt concentration as predicted by the Poisson and Nernst-Planck equations. Furthermore, our measurements show that ΔR/R(0) goes to zero when the tip is about five times the pore diameter away from the center of the pore entrance. The results in this work not only demonstrate a way to probe the access resistance of nanopores experimentally, they also provide a way to locate the nanopore in salt solution, and open the door to future nanopore experiments for detecting single biomolecules attached to a probe tip.

Towards in vitro molecular diagnostics using nanostructures

Nanostructures appear to be promising for a number of applications in molecular diagnostics, mainly due to the increased surface-to-volume ratio they can offer, the very low limit of detection achievable, and the possibility to fabricate point-of-care diagnostic devices. In this paper, we review examples of the use of nanostructures as diagnostic tools that bring in marked improvements over prevalent classical assays. The focus is laid on the various sensing paradigms that possess the potential or have demonstrated the capability to replace or augment current analytical strategies. We start with a brief introduction of the various types of nanostructures and their physical properties that determine the transduction principle. This is followed by a concise collection of various functionalization protocols used to immobilize biomolecules on the nanostructure surface. The sensing paradigms are discussed in two contexts: the nanostructure acting as a label for detection, or the nanostructure acting as a support upon which the molecular recognition events take place. In order to be successful in the field of molecular diagnostics, it is important that the nanoanalytical tools be evaluated in the appropriate biological environment. The final section of the review compiles such examples, where the nanostructure-based diagnostic tools have been tested on realistic samples such as serum, demonstrating their analytical power even in the presence of complex matrix effects. The ability of nanodiagnostic tools to detect ultralow concentrations of one or more analytes coupled with portability and the use of low sample volumes is expected to have a broad impact in the field of molecular diagnostics.

DNA origami nanopores

We demonstrate the assembly of functional hybrid nanopores for single molecule sensing by inserting DNA origami structures into solid-state nanopores. In our experiments, single artificial nanopores based on DNA origami are repeatedly inserted in and ejected from solid-state nanopores with diameters around 15 nm. We show that these hybrid nanopores can be employed for the detection of λ-DNA molecules. Our approach paves the way for future development of adaptable single-molecule nanopore sensors based on the combination of solid-state nanopores and DNA self-assembly.

Graphene nanopore devices for DNA sensing

We describe here a method for detecting the translocation of individual DNA molecules through nanopores created in graphene membranes. The devices consist of 1-5-nm thick graphene membranes with electron-beam sculpted nanopores from 5 to 10 nm in diameter. Due to the thin nature of the graphene membranes, and the reduced electrical resistance, we observe larger blocked currents than for traditional solid-state nanopores. We also show how ionic current noise levels can be reduced with the atomic-layer deposition of a few nanometers of titanium dioxide over the graphene surface. Unlike traditional solid-state nanopore materials that are insulating, graphene is an excellent electrical conductor, and its use opens the door to a new future class of nanopore devices in which electronic sensing and control is performed directly at the pore.

Optical tweezers for mechanical control over DNA in a nanopore

The translocation of long-chain molecules, such as DNA or peptides, through membranes is an integral process for the function of living cells. During the translocation process, a number of interactions of electrostatic or hydrophobic nature govern the translocation velocity. Most of these interactions remain largely unexplored on the single-molecule level due to a lack of suitable instrumentation. We have shown that a combination of optical tweezers, single solid-state nanopores, and electrophysiological ionic current detection can provide further insight into the behavior of polymers in confinement. Here, we describe the experimental procedures necessary for manipulation of single biopolymers in a single nanopore not only by electrical fields, but also through mechanical forces using optical tweezers.

DNA characterization by transverse electrical current in a nanochannel

We review an approach for the characterization of single-stranded DNA based on the statistical identification of single bases via transverse electronic transport while DNA translocates in a nanopore or nanochannel. We describe the theoretical methods used to demonstrate this method for experimentally realizable systems and discuss the different physical processes involved. Recent experimental reports have shown the validity of this approach, although further work is necessary to make this a practical fast sequencing tool.

DNA unzipping and protein unfolding using nanopores

We present here an overview on unfolding of biomolecular structures as DNA double strands or protein folds. After some theoretical considerations giving orders of magnitude about transport timescales through pores, forces involved in unzipping processes … we present our experiments on DNA unzipping or protein unfolding using a nanopore. We point out the difficulties that can be encountered during these experiments, such as the signal analysis problems, noise issues, or experimental limitations of such system.

Passive and electrically actuated solid-state nanopores for sensing and manipulating DNA

Solid-state nanopores have emerged as powerful new tools for electrically characterizing single DNA molecules. When DNA molecules are made to rapidly translocate a nanopore by electrophoresis, the resulting ionic current blockage provides information about the molecular length and folding conformation. A solid-state nanopore can also be integrated with nanofabricated actuators and sensors, such as an embedded gate electrode or transverse tunneling electrodes, to enhance its functionality. Here we describe detailed methods for fabricating passive solid-state nanopores and using them to detect DNA translocations. We also describe procedures for integrating electrodes into the nanopore membrane in order to create an electrically active structure. Finally, we describe how to modulate the ionic conductance through a pore whose inner surface is surrounded by an embedded annular gate electrode.

DNA characterization with ion beam-sculpted silicon nitride nanopores

Solid-state nanopores are emerging as robust single molecule electronic measurement devices and as platforms for confining biomolecules for further analysis. The first silicon nitride nanopore to detect individual DNA molecules was fabricated using ion beam sculpting (IBS), a method that uses broad, low-energy ion beams to create nanopores with dimensions ranging from 2 to 20 nm. In this chapter, we discuss the fabrication, characterization, and use of IBS-sculpted nanopores as well as efficient uses of pClamp and MATLAB software suites for data acquisition and analysis. The fabrication section covers the repeatability and the pore size limits. The characterization discussion focuses on the geometric properties as measured by low- and high-resolution transmission electron microscopy (TEM), electron energy loss spectroscopy, and energy-filtered TEM. The section on translocation experiments focuses on how to use tools commonly available to the nanopore experimenter to determine whether a pore will be useful for experimentation or if it should be abandoned. A memory-efficient method of taking data using Clampex's event-driven mode and dual-channel recording is presented, followed by an easy-to-implement multithreshold event detection and classification method using MATLAB software.

Measurements of DNA immobilized in the alpha-hemolysin nanopore

In the past decade, there have been extensive studies aimed at exploring the potential of protein nanopores to sequence single strands of DNA using resistive pulse sensing. The high speed of DNA electrophoretically driven through these pores (∼l μs/base) necessitates high bandwidth measurements, which prevent resolution of the picoampere differences in blockage current resulting from different nucleotides. Here, we describe a procedure for the immobilization of DNA in the α-hemolysin protein nanopore which enables low-noise, high-precision measurements capable of resolving subpicoampere differences in blockage current associated with differences in the sequence and structure of the DNA.

DNA sequencing by nanopore-induced photon emission

Nanopore-based DNA analysis is an extremely attractive area of research due to the simplicity of the method, and the ability to not only probe individual molecules, but also to detect very small amounts of genomic material. Here, we describe the materials and methods of a novel, nanopore-based, single-molecule DNA sequencing system that utilizes optical detection. We convert target DNA according to a binary code, which is recognized by molecular beacons with two types of fluorophores. Solid-state nanopores are then used to sequentially strip off the beacons, leading to a series of photon bursts that can be detected with a custom-made microscope. We do not use any enzymes in the readout stage; thus, our system is not limited by the highly variable processivity, lifetime, and inaccuracy of individual enzymes that can hinder throughput and reliability. Furthermore, because our system uses purely optical readout, we can take advantage of high-end, wide-field imaging devices to record from multiple nanopores simultaneously. This allows an extremely straightforward parallelization of our system to nanopore arrays.

Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores

Molecular dynamics (MD) simulations have become a standard method for the rational design and interpretation of experimental studies of DNA translocation through nanopores. The MD method, however, offers a multitude of algorithms, parameters, and other protocol choices that can affect the accuracy of the resulting data as well as computational efficiency. In this chapter, we examine the most popular choices offered by the MD method, seeking an optimal set of parameters that enable the most computationally efficient and accurate simulations of DNA and ion transport through biological nanopores. In particular, we examine the influence of short-range cutoff, integration timestep and force field parameters on the temperature and concentration dependence of bulk ion conductivity, ion pairing, ion solvation energy, DNA structure, DNA-ion interactions, and the ionic current through a nanopore.

Local electrical potential detection of DNA by nanowire-nanopore sensors

Nanopores could potentially be used to perform single-molecule DNA sequencing at low cost and with high throughput. Although single base resolution and differentiation have been demonstrated with nanopores using ionic current measurements, direct sequencing has not been achieved because of the difficulties in recording very small (∼pA) ionic currents at a bandwidth consistent with fast translocation speeds. Here, we show that solid-state nanopores can be combined with silicon nanowire field-effect transistors to create sensors in which detection is localized and self-aligned at the nanopore. Well-defined field-effect transistor signals associated with DNA translocation are recorded when an ionic strength gradient is imposed across the nanopores. Measurements and modelling show that field-effect transistor signals are generated by highly localized changes in the electrical potential during DNA translocation, and that nanowire-nanopore sensors could enable large-scale integration with a high intrinsic bandwidth.

Monitoring protein adsorption with solid-state nanopores

Solid-state nanopores have been used to perform measurements at the single-molecule level to examine the local structure and flexibility of nucleic acids, the unfolding of proteins, and binding affinity of different ligands. By coupling these nanopores to the resistive-pulse technique, such measurements can be done under a wide variety of conditions and without the need for labeling. In the resistive-pulse technique, an ionic salt solution is introduced on both sides of the nanopore. Therefore, ions are driven from one side of the chamber to the other by an applied transmembrane potential, resulting in a steady current. The partitioning of an analyte into the nanopore causes a well-defined deflection in this current, which can be analyzed to extract single-molecule information. Using this technique, the adsorption of single proteins to the nanopore walls can be monitored under a wide range of conditions. Protein adsorption is growing in importance, because as microfluidic devices shrink in size, the interaction of these systems with single proteins becomes a concern. This protocol describes a rapid assay for protein binding to nitride films, which can readily be extended to other thin films amenable to nanopore drilling, or to functionalized nitride surfaces. A variety of proteins may be explored under a wide range of solutions and denaturing conditions. Additionally, this protocol may be used to explore more basic problems using nanopore spectroscopy.

Computational investigation of DNA detection using graphene nanopores

Nanopore-based single-molecule detection and analysis have been pursued intensively over the past decade. One of the most promising applications in this regard is DNA sequencing achieved through DNA translocation-induced blockades in ionic current. Recently, nanopores fabricated in graphene sheets were used to detect double-stranded DNA. Due to its subnanometer thickness, graphene nanopores show great potential to realize DNA sequencing at single-base resolution. Resolving at the atomic level electric field-driven DNA translocation through graphene nanopores is crucial to guide the design of graphene-based sequencing devices. Molecular dynamics simulations, in principle, can achieve such resolution and are employed here to investigate the effects of applied voltage, DNA conformation, and sequence as well as pore charge on the translocation characteristics of DNA. We demonstrate that such simulations yield current characteristics consistent with recent measurements and suggest that under suitable bias conditions A-T and G-C base pairs can be discriminated using graphene nanopores.

DIRECT FORMATION OF NANOPORE ARRAY VIA FOCUSED ION BEAM FINE MILLING AND SURFACE COATING TECHNIQUES

A nanopore array with diameter of ~30 nm was fabricated by use of focused ion beam (FIB) scanning and thin film coating on Si (100). A thin film of SiO 2 with thickness of 200 nm (used as a sacrificial layer) was coated by physical evaporation deposition (PVD) first. Next, the thin films of poly-silicon with thickness of 50 nm were coated on double side of the substrate. A window with an area of 2 × 2 mm 2 was opened by reactive ion etching from bottom side and reached to the thin film of SiO 2. After that, a fine controlled FIB milling with bitmap function (milling according to a designed pattern in a defined area) was used to scan the area. Signal is obtained by a sensor inside the vacuum chamber collecting secondary electrons emitted from the sputtered material when the beam reach the layer of SiO 2. Stopping the milling process at this moment, the nanopore array was derived after removing the sacrificial layer by wet chemical etching. The nanopore arrays were characterized using transmission electron microscopy (TEM) after the FIB drilling.

MOLECULAR TRANSPORT AND FLUIDICS IN CARBON NANOTUBE

In this article we review recent developments in molecular transport and fluidics in carbon nanotube (CNT)-based nanochannels. Atomic molecular dynamics simulations and theoretical studies based on Fokker–Planck diffusion equation on the transport of large and long polymer molecules in CNTs are the focus of the article. Fast translocation and diffusion processes of large molecules in CNTs are reviewed and discussed, considering the effects of interfacial interactions and molecular conformations and structures at interface. The transport features for multiple molecules diffusing through CNTs are also discussed.

Nanofluidic devices with two pores in series for resistive-pulse sensing of single virus capsids

We report fabrication and characterization of nanochannel devices with two nanopores in series for resistive-pulse sensing of hepatitis B virus (HBV) capsids. The nanochannel and two pores are patterned by electron beam lithography between two microchannels and etched by reactive ion etching. The two nanopores are 50-nm wide, 50-nm deep, and 40-nm long and are spaced 2.0-μm apart. The nanochannel that brackets the two pores is 20× wider (1 μm) to reduce the electrical resistance adjacent to the two pores and to ensure the current returns to its baseline value between resistive-pulse events. Average pulse amplitudes differ by <2% between the two pores and demonstrate that the fabrication technique is able to produce pores with nearly identical geometries. Because the two nanopores in series sense single particles at two discrete locations, particle properties, e.g., electrophoretic mobility, are determined from the pore-to-pore transit time.

Electrophoretic time-of-flight measurements of single DNA molecules with two stacked nanopores

Electrophoretic transport through a solid-state nanodevice comprised of two stacked nanopore sensors is used to determine the free-solution mobility of DNA molecules based on their "time-of-flight" between the two pores. Mobility measurements are possible at very low (100 pM) DNA concentration and for low as well as high salt concentrations (here 30 mM and 1 M KCl). The mechanism of DNA transport through the device is elucidated by statistical analysis, showing the free-draining nature of the translocating DNA polymers and a barrier-dominated escape through the second pore. Furthermore, consecutive threading of single molecules through the two pores can be used to gain more detailed information on the dynamics of the molecules by correlation analysis, which also provides a direct electrical proof for translocation.

SEM-induced shrinking of solid-state nanopores for single molecule detection

We have investigated the mechanism by which the diameter of solid-state nanopores is reduced by a scanning electron microscope. The process depends on beam parameters such as the accelerating voltage and electron flux and does not involve simple electron-beam-induced deposition of hydrocarbon contaminants. Instead, it is an energy-dependent process that involves material flow along the surface of the nanopore membrane. We also show that pores fabricated in this manner can detect double stranded DNA.

Origins and consequences of velocity fluctuations during DNA passage through a nanopore

We describe experiments and modeling results that reveal and explain the distribution of times that identical double-stranded DNA (dsDNA) molecules take to pass through a voltage-biased solid-state nanopore. We show that the observed spread in this distribution is caused by viscous-drag-induced velocity fluctuations that are correlated with the initial conformation of nanopore-captured molecules. This contribution exceeds that due to diffusional Brownian motion during the passage. Nevertheless, and somewhat counterintuitively, the diffusional Brownian motion determines the fundamental limitations of rapid DNA strand sequencing with a nanopore. We model both diffusional and conformational fluctuations in a Langevin description. It accounts well for passage time variations for DNA molecules of different lengths, and predicts conditions required for low-error-rate nanopore-strand DNA sequencing with nanopores.

Translocation of single-stranded DNA through the α-hemolysin protein nanopore in acidic solutions

The effect of acidic pH on the translocation of single-stranded DNA through the α-hemolysin pore is investigated. Two significantly different types of events, i.e. deep blockades and shallow blockades, are observed at low pH. The residence times of the shallow blockades are not significantly different from those of the DNA translocation events obtained at or near physiological pH, whereas the deep blockades have much larger residence times and blockage amplitudes. With a decrease in the pH of the electrolyte solution, the percentage of the deep blockades in the total events increases. Furthermore, the mean residence time of these long-lived events is dependent on the length of DNA, and also varies with the nucleotide base, suggesting that they are appropriate for use in DNA analysis. In addition to being used as an effective approach to affect DNA translocation in the nanopore, manipulation of the pH of the electrolyte solution provides a potential means to greatly enhance the sensitivity of nanopore stochastic sensing.

Resizing metal-coated nanopores using a scanning electron microscope

Electron beam-induced shrinkage provides a convenient way of resizing solid-state nanopores in Si(3) N(4) membranes. Here, a scanning electron microscope (SEM) has been used to resize a range of different focussed ion beam-milled nanopores in Al-coated Si(3) N(4) membranes. Energy-dispersive X-ray spectra and SEM images acquired during resizing highlight that a time-variant carbon deposition process is the dominant mechanism of pore shrinkage, although granular structures on the membrane surface in the vicinity of the pores suggest that competing processes may occur. Shrinkage is observed on the Al side of the pore as well as on the Si(3) N(4) side, while the shrinkage rate is observed to be dependent on a variety of factors.

Advances in Resistive Pulse Sensors: Devices bridging the void between molecular and microscopic detection

Since the first reported use of a biological ion channel to detect differences in single stranded genomic base pairs in 1996, a renaissance in nanoscale resistive pulse sensors has ensued. This resurgence of a technique originally outlined and commercialized over fifty years ago has largely been driven by advances in nanoscaled fabrication, and ultimately, the prospect of a rapid and inexpensive means for genomic sequencing as well as other macromolecular characterization. In this pursuit, the potential application of these devices to characterize additional properties such as the size, shape, charge, and concentration of nanoscaled materials (10 - 900 nm) has been largely overlooked. Advances in nanotechnology and biotechnology are driving the need for simple yet sensitive individual object readout devices such as resistive pulse sensors. This review will examine the recent progress in pore-based sensing in the nanoscale range. A detailed analysis of three new types of pore sensors - in-series, parallel, and size-tunable pores - has been included. These pores offer improved measurement sensitivity over a wider particle size range. The fundamental physical chemistry of these techniques, which is still evolving, will be reviewed.

Nanopore sensors for nucleic acid analysis

Nanopore analysis is an emerging technique that involves using a voltage to drive molecules through a nanoscale pore in a membrane between two electrolytes, and monitoring how the ionic current through the nanopore changes as single molecules pass through it. This approach allows charged polymers (including single-stranded DNA, double-stranded DNA and RNA) to be analysed with subnanometre resolution and without the need for labels or amplification. Recent advances suggest that nanopore-based sensors could be competitive with other third-generation DNA sequencing technologies, and may be able to rapidly and reliably sequence the human genome for under $1,000. In this article we review the use of nanopore technology in DNA sequencing, genetics and medical diagnostics.

DNA detection with a polymeric nanochannel device

We present the development and the electrical characterization of a polymeric nanochannel device. Standard microfabrication coupled to Focused Ion Beam (FIB) nanofabrication is used to fabricate a silicon master, which can be then replicated in a polymeric material by soft lithography. Such an elastomeric nanochannel device is used to study DNA translocation events during electrophoresis experiments. Our results demonstrate that an easy and low cost fabrication technique allows creation of a low noise device for single molecule analysis.

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.

Ultrasmall silver nanopores fabricated by femtosecond laser pulses

Ultrasmall nanopores in silver thin films with a diameter of about 2 nm have been fabricated using femtosecond laser ablation in liquid. Ultrafast laser pulse ablation generates highly nonequilibrium excitated states, from which silver thin films emerge and progressively grow with the assistance of capping agent molecules. During this growth process, capping agent molecules are enclaved within the film, leaving individual ultrasmall pores in the thin film. Our first-principles calculations show that the pore size is critically determined by the dimension of the confined molecules. Our approach advances the capability of optical methods in making nanoscale structures with potential applications in areas such as near-field aperture probes, imaging masks, magnetic plasmonic resonances, and biosensing with individual nanopores.

Translocation of DNA molecules through nanopores with salt gradients: the role of osmotic flow

Recent experiments of translocation of double-stranded DNA through nanopores [M. Wanunu et al., Nature Nanotech. 5, 160 (2009)] reveal that the DNA capture rate can be significantly influenced by a salt gradient across the pore. We show that osmotic flow combined with electrophoretic effects can quantitatively explain the experimental data on the salt-gradient dependence of the capture rate.

Force-driven polymer translocation through a nanopore: an old problem revisited

We consider DNA translocation through a pore in a planar membrane. The pore is so narrow that only one DNA segment can fit in. Assuming that the biasing force f acts inside the pore only, and that the DNA monomer number N is asymptotically large, we modify the previously developed treatment of the stretched part of the pre-translocated polymer by introducing the concept of "iso-flux trumpet". We show that friction of a moving chain in the trumpet, although it determines the speed of the process, provides only a marginal fraction of overall dissipation in the process. The dominant dissipation turns out to be due to irreversible entropic squeezing of the chain into the small pore. We also discover that because of the role of the membrane a much larger amount of heat of order k(B)T per monomer gets transferred from the heat bath on the post-translocation side to that on the pre-translocation side.

Effects of electrons on the shape of nanopores prepared by focused electron beam induced etching

The fabrication of nanometric pores with controlled size is important for applications such as single molecule detection. We have recently suggested the use of focused electron beam induced etching (FEBIE) for the preparation of such nanopores in silicon nitride membranes. The use of a scanning probe microscope as the electron beam source makes this technique comparably accessible, opening the way to widespread fabrication of nanopores. Since the shape of the nanopores is critically important for their performance, in this work we focus on its analysis and study the dependence of the nanopore shape on the electron beam acceleration voltage. We show that the nanopore adopts a funnel-like shape, with a central pore penetrating the entire membrane, surrounded by an extended shallow-etched region at the top of the membrane. While the internal nanopore size was found to depend on the electron acceleration voltage, the nanopore edges extended beyond the primary electron beam spot size due to long-range effects, such as radiolysis and diffusion. Moreover, the size of the peripheral-etched region was found to be less dependent on the acceleration voltage. We also found that chemical etching is the rate-limiting step of the process and is only slightly dependent on the acceleration voltage. Furthermore, due to the chemical etch process the chemical composition of the nanopore rims was found to maintain the bulk membrane composition.