Ion-beam sculpting at nanometre length scales

Nanopore sculpting with noble gas ions

We demonstrate that 3 keV ion beams, formed from the common noble gasses, He, Ne, Ar, Kr, and Xe, can controllably "sculpt" nanometer scale pores in silicon nitride films. Single nanometer control of structural dimensions in nanopores can be achieved with all ion species despite a very wide range of sputtering yields and surface energy depositions. Heavy ions shrink pores more efficiently and make thinner pores than lighter ions. The dynamics of nanopore closing is reported for each ion species and the results are fitted to an adatom diffusion model with excellent success. We also present an experimental method for profiling the thickness of the local membrane around the nanopore based on low temperature sputtering and data is presented that provides quantitative measurements of the thickness and its dependence on ion beam species.

Biosensing with conically shaped nanopores and nanotubes

In this review we consider recent results from our group that are directed towards developing "smart" synthetic nanopores that can mimic the functions of biological nanopores (transmembrane proteins). We first discuss the preparation and characterization of conical nanopores synthesized using the track-etch process. We then consider the design and function of conical nanopores that can rectify the ionic current that flows through these pores under an applied transmembrane potential. Finally, two types of sensors that we have developed with these conical nanopores are described. The first sensor makes use of molecular recognition elements that are bound to the nanopore mouth to selectively block the nanopore tip, thus detecting the presence of the analyte. The second sensor makes use of conical nanopores in a resistive-pulse type experiment, detecting the analyte via transient blockages in ionic current.

Nanofluidic channels fabrication and manipulation of DNA molecules

Nanofluidic channel arrays, which have a width of about 40 nm, depth of 60 nm and length of 50 mum, were created using a focused-ion-beam milling instrument on a silicon nitride film swiftly and exactly, as is necessary. Stained -DNA molecules were put inside these sub-100 nm conduits by capillary force and they were stretched and transferred along these conduits, which were dealt with activating reagent Brij aqueous solution in advance. The movements of DNA molecules in these channels were discussed. These nano-structure channels may be useful in the study and analysis of the statics as well as the dynamics of single biomolecules.

Fabrication and characterization of nanopore-based electrodes with radii down to 2 nm

We report on the fabrication and characterization of gold nanoelectrodes with carefully controlled nanometer dimensions in a matrix of insulating silicon nitride. A focused electron beam was employed to drill nanopores in a thin silicon nitride membrane. The size and shape of the nanopores were studied with high-resolution transmission electron microscopy and electron-energy-loss two-dimensional maps. The pores were subsequently filled with gold, yielding conically shaped nanoelectrodes. The nanoelectrodes were examined by atomic and electrostatic force microscopy. Their applicability in electrochemistry was demonstrated by steady-state cyclic voltammetry. Pores with a radii down to 0.4 nm and electrodes with radii down to 2 nm are demonstrated.

Modeling of the bioactivated nanopore devices

This paper presents the modeling of the electrical properties of bioactivated nanopores, customized nanopore devices with a biological macromolecule attached in the pore as the probe. These devices are capable of detecting and analyzing interactions between the attached biomolecule and the molecules in the analyte at a single molecule level.

Salt dependence of ion transport and DNA translocation through solid-state nanopores

We report experimental measurements of the salt dependence of ion transport and DNA translocation through solid-state nanopores. The ionic conductance shows a three-order-of-magnitude decrease with decreasing salt concentrations from 1 M to 1 muM, strongly deviating from bulk linear behavior. The data are described by a model that accounts for a salt-dependent surface charge of the pore. Subsequently, we measure translocation of 16.5-mum-long dsDNA for 50 mM to 1 M salt concentrations. DNA translocation is shown to result in either a decrease ([KCl] > 0.4 M) or increase of the ionic current ([KCl] < 0.4 M). The data are described by a model where current decreases result from the partial blocking of the pore and current increases are attributed to motion of the counterions that screen the charge of the DNA backbone. We demonstrate that the two competing effects cancel at a KCl concentration of 370 +/- 40 mM.

Compression and free expansion of single DNA molecules in nanochannels

We investigated compression and ensuing expansion of long DNA molecules confined in nanochannels. Transverse confinement of DNA molecules in the nanofluidic channels leads to elongation of their unconstrained equilibrium configuration. The extended molecules were compressed by electrophoretically driving them into porelike constrictions inside the nanochannels. When the electric field was turned off, the DNA strands expanded. This expansion, the dynamics of which has not previously been observable in artificial systems, is explained by a model that is a variation of de Gennes's polymer model.

Translocation of structured polynucleotides through nanopores

We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic barriers for the translocation process. We show that this circumstance may be exploited to determine the full basepairing pattern of polynucleotides, including RNA pseudoknots. The crucial requirement is that the translocation dynamics (i.e. the length of the translocated molecular segment) needs to be recorded as a function of time with a spatial resolution of a few nucleotides. This could be achieved, for instance, by applying a mechanical driving force for translocation and recording force-extension curves (FECs) with a device such as an atomic force microscope or optical tweezers. Our analysis suggests that, with this added spatial resolution, nanopores could be transformed into a powerful experimental tool to study the folding of nucleic acids.

Probing nanotube-nanopore interactions

We demonstrate a new nanoscale system consisting of a nanotube threaded through a nanopore in aqueous solution. Its electrical and mechanical properties are sensitive to experimentally controllable conformational changes on sub-Angstrom length scales. Ionic current transport through a nanopore is significantly suppressed by the threading nanotube and the mechanical interactions between the nanotube and pore are accounted for by a folding geometry. The experiments provide first measurements of the longitudinal resolution and metrology of a solid-state nanopore "microscope." This new nanostructure provides a means to study molecule-nanotube interactions in conducting ionic solutions as well as geometrical and surface properties of nanopores and nanotubes.

Coupled dynamics of RNA folding and nanopore translocation

The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base pairing theoretically, using kinetic Monte Carlo simulations and analytical methods. We find that the transient formation of base pairs that do not occur in the ground state can significantly speed up translocation.

Focused ion beam characterization of plasma-assisted deposition on polymer films at the nanoscale

In this paper, a novel technique is presented for the characterization at the nanoscale of plasma-assisted deposit on polyethylene-terephthalate (PET) polymer films. In previous studies, some microcharacterization and morphology analyses of plasma-assisted deposition were performed by atomic force microscopy (AFM). In the work presented here, we analysed the thickness and homogeneity of plasma-assisted deposits by focused ion beam (FIB). This technique with 5-7 nm resolution requires no sample preparation and relies on a sequence of operations on a relatively fast time scale, so that it is easy to make thorough investigations of the sample. We performed electron and ion imaging of the surface of the material, and a subsequent ionic cutting allowed the study of the morphology of the same sample. We developed a novel approach to the edge detection techniques (EDT) in images for a fast evaluation and monitoring of the deposited layer.

Micro-separation toward systems biology

Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.

Shocks in Ion Sputtering Sharpen Steep Surface Features

We report a regime of ion beam sputtering that occurs for sufficiently steep slopes. High slopes propagate over large distances without dissipating the steepest features. Both the propagation velocity and the dynamically selected slope are universal, independent of the details of the initial shape of the surface. The resulting behavior can be understood as the propagation of a shock front that self-selects a stable slope, as has been previously observed in thin-film fluid flows. Experiments confirm predictions of the theory. An important implication of the propagative behavior at high surface slopes is that a pattern can be fabricated at a large length scale and, through uniform ion irradiation, reduced to a smaller length scale while preserving, or even sharpening, the sharpest features.

Conductance of ion channels and nanopores with charged walls: a toy model

We consider ion transport through protein ion channels in lipid membranes and water-filled nanopores in silicon films. It is known that, due to the large ratio of dielectric constants of water and the surrounding material, an ion placed inside the channel faces a large electrostatic self-energy barrier. The barrier leads to an exponentially large resistance of the channel. We study reduction of the electrostatic barrier by immobile charges located on the internal walls of the channel. We show that the barrier practically vanishes already at relatively small concentration of wall charges.

Streaming currents in a single nanofluidic channel

We report measurements of the streaming current, an electrical current generated by a pressure-driven liquid flow, in individual rectangular silica nanochannels down to 70 nm in height. The streaming current is observed to be proportional to the pressure gradient and increases with the channel height. As a function of salt concentration, it is approximately constant below approximately 10 mM, whereas it strongly decreases at higher salt. Changing the sign of the surface charge is found to reverse the streaming current. The data are best modeled using a nonlinear Poisson-Boltzmann theory that includes the salt-dependent hydration state of the silica surface.

Slowing DNA translocation in a solid-state nanopore

Reducing a DNA molecule's translocation speed in a solid-state nanopore is a key step toward rapid single molecule identification. Here we demonstrate that DNA translocation speeds can be reduced by an order of magnitude over previous results. By controlling the electrolyte temperature, salt concentration, viscosity, and the electrical bias voltage across the nanopore, we obtain a 3 base/micros translocation speed for 3 kbp double-stranded DNA in a 4-8 nm diameter silicon nitride pore. Our results also indicate that the ionic conductivity inside such a nanopore is smaller than it is in bulk.

DNA translocation in inorganic nanotubes

Inorganic nanotubes were successfully integrated with microfluidic systems to create nanofluidic devices for single DNA molecule sensing. Inorganic nanotubes are unique in their high aspect ratio and exhibit translocation characteristics in which the DNA is fully stretched. Transient changes of ionic current indicate DNA translocation events. A transition from current decrease to current enhancement during translocation was observed on changing the buffer concentration, suggesting interplay between electrostatic charge and geometric blockage effects. These inorganic nanotube nanofluidic devices represent a new platform for the study of single biomolecule translocation with the potential for integration into nanofluidic circuits.

Miniaturization in functional genomics and proteomics

Proteins are the key components of the cellular machinery responsible for processing changes that are ordered by genomic information. Analysis of most human proteins and nucleic acids is important in order to decode the complex networks that are likely to underlie many common diseases. Significant improvements in current technology are also required to dissect the regulatory processes in high-throughtput and with low cost. Miniaturization of biological assays is an important prerequisite to achieve these goals in the near future.

Conductance and ion selectivity of a mesoscopic protein nanopore probed with cysteine scanning mutagenesis

Nanometer-scale proteinaceous pores are the basis of ion and macromolecular transport in cells and organelles. Recent studies suggest that ion channels and synthetic nanopores may prove useful in biotechnological applications. To better understand the structure-function relationship of nanopores, we are studying the ion-conducting properties of channels formed by wild-type and genetically engineered versions of Staphylococcus aureus alpha-hemolysin (alphaHL) reconstituted into planar lipid bilayer membranes. Specifically, we measured the ion selectivities and current-voltage relationships of channels formed with 24 different alphaHL point cysteine mutants before and after derivatizing the cysteines with positively and negatively charged sulfhydryl-specific reagents. Novel negative charges convert the selectivity of the channel from weakly anionic to strongly cationic, and new positive charges increase the anionic selectivity. However, the extent of these changes depends on the channel radius at the position of the novel charge (predominantly affects ion selectivity) or on the location of these charges along the longitudinal axis of the channel (mainly alters the conductance-voltage curve). The results suggest that the net charge of the pore wall is responsible for cation-anion selectivity of the alphaHL channel and that the charge at the pore entrances is the main factor that determines the shape of the conductance-voltage curves.

Electrolytic transport through a synthetic nanometer-diameter pore

We have produced single, synthetic nanometer-diameter pores by using a tightly focused, high-energy electron beam to sputter atoms in 10-nm-thick silicon nitride membranes. Subsequently, we measured the ionic conductance as a function of time, bath concentration, and pore diameter to infer the conductivity and ionic mobility through the pores. The pore conductivity is found to be much larger than the bulk conductivity for dilute bath concentrations, where the Debye length is larger than the pore radius, whereas it is comparable with or less than the bulk for high bath concentrations. We interpret these observations by using multiscale simulations of the ion transport through the pores. Molecular dynamics is used to estimate the ion mobility, and ion transport in the pore is described by the coupled Poisson-Nernst-Planck and the Stokes equations that are solved self-consistently for the ion concentration and velocity and electrical potential. We find that the measurements are consistent with the presence of fixed negative charge in the pore wall and a reduction of the ion mobility because of the fixed charge and the ion proximity to the pore wall.

Fast DNA translocation through a solid-state nanopore

We report experiments and modeling of translocation of double-strand DNA through a siliconoxide nanopore. Long DNA molecules with different lengths ranging from 6500 to 97000 base pairs have been electrophoretically driven through a 10 nm pore. We observe a power-law caling of the translocation time with the length, with an exponent of 1.27. This nonlinear scaling is strikingly different from the well-studied linear behavior observed in similar experiments performed on protein pores. We present a theoretical model where hydrodynamic drag on the ection of the polymer outside the pore is the dominant force counteracting the electrical driving force. We show that this applies to our experiments, and we derive a power-law scaling with an exponent of 1.22, in good agreement with the data.

The nanopore connection to cell membrane unitary permeability

Artificial nanopores have recently emerged as versatile tools for analyzing and sorting single molecules at high speed. However, the biological cell has already developed a large set of sophisticated protein nanopores that are able to selectively translocate all types of molecules through membranes. Therefore, hybrid devices combining artifical solid-state with biomimetic protein nanopores appear to us as a particularly promising approach to the creation of powerful diagnostic, preparative and therapeutic devices. Here, we discuss a technique, optical single-transporter recording (OSTR), in which arrays of artificial micropores and nanopores are employed to analyze protein nanopores of cellular membranes. After briefly summarizing some salient features of OSTR, the technique is compared with the electrical patch clamp method and the first results of our efforts to amalgamate optical and electrical recording are described. Finally, prospects for combining OSTR with 4Pi microscopy, single-molecule fluorescence spectroscopy and fluorescence correlation spectroscopy are discussed.

Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map

alpha-Hemolysin of Staphylococcus aureus is a self-assembling toxin that forms a water-filled transmembrane channel upon oligomerization in a lipid membrane. Apart from being one of the best-studied toxins of bacterial origin, alpha-hemolysin is the principal component in several biotechnological applications, including systems for controlled delivery of small solutes across lipid membranes, stochastic sensors for small solutes, and an alternative to conventional technology for DNA sequencing. Through large-scale molecular dynamics simulations, we studied the permeability of the alpha-hemolysin/lipid bilayer complex for water and ions. The studied system, composed of approximately 300,000 atoms, included one copy of the protein, a patch of a DPPC lipid bilayer, and a 1 M water solution of KCl. Monitoring the fluctuations of the pore structure revealed an asymmetric, on average, cross section of the alpha-hemolysin stem. Applying external electrostatic fields produced a transmembrane ionic current; repeating simulations at several voltage biases yielded a current/voltage curve of alpha-hemolysin and a set of electrostatic potential maps. The selectivity of alpha-hemolysin to Cl(-) was found to depend on the direction and the magnitude of the applied voltage bias. The results of our simulations are in excellent quantitative agreement with available experimental data. Analyzing trajectories of all water molecule, we computed the alpha-hemolysin's osmotic permeability for water as well as its electroosmotic effect, and characterized the permeability of its seven side channels. The side channels were found to connect seven His-144 residues surrounding the stem of the protein to the bulk solution; the protonation of these residues was observed to affect the ion conductance, suggesting the seven His-144 to comprise the pH sensor that gates conductance of the alpha-hemolysin channel.

Advances in sequencing technology

Faster sequencing methods will undoubtedly lead to faster single nucleotide polymorphism (SNP) discovery. The Sanger method has served as the cornerstone for genome sequence production since 1977, close to almost 30 years of tremendous utility [Sanger, F., Nicklen, S., Coulson, A.R, DNA sequencing with chain-terminating inhibitors, Proc. Natl. Acad. Sci. U.S.A. 74 (1977) 5463-5467]. With the completion of the human genome sequence [Venter, J.C. et al., The sequence of the human genome, Science 291 (2001) 1304-1351; Lander, E.S. et al., Initial sequencing and analysis of the human genome, Nature 409 (2001) 860-921], there is now a focus on developing new sequencing methodologies that will enable "personal genomics", or the routine study of our individual genomes. Technologies that will lead us to this lofty goal are those that can provide improvements in three areas: read length, throughput, and cost. As progress is made in this field, large sections of genomes and then whole genomes of individuals will become increasingly more facile to sequence. SNP discovery efforts will be enhanced lock-step with these improvements. Here, the breadth of new sequencing approaches will be summarized including their status and prospects for enabling personal genomics.

Translocation of double-strand DNA through a silicon oxide nanopore

We report double-strand DNA translocation experiments using silicon oxide nanopores with a diameter of about 10 nm . By monitoring the conductance of a voltage-biased pore, we detect molecules with a length ranging from 6557 to 48 500 base pairs. We find that the molecules can pass the pore both in a straight linear fashion and in a folded state. Experiments on circular DNA further support this picture. We sort the molecular events according to their folding state and estimate the folding position. As a proof-of-principle experiment, we show that a nanopore can be used to distinguish the lengths of DNA fragments present in a mixture. These experiments pave the way for quantitative analytical techniques with solid-state nanopores.

What is nanomedicine?

The early genesis of the concept of nanomedicine sprang from the visionary idea that tiny nanorobots and related machines could be designed, manufactured, and introduced into the human body to perform cellular repairs at the molecular level. Nanomedicine today has branched out in hundreds of different directions, each of them embodying the key insight that the ability to structure materials and devices at the molecular scale can bring enormous immediate benefits in the research and practice of medicine.

An analysis of mismatched duplex DNA unzipping through a bacterial nanopore

A 50-base Guide strand was synthesized that consisted of a central 10-base probe sequence flanked by two tracts of 20 adenine residues. Target sequences of 10 bases containing up to three mismatches were prepared and hybridized to the Guide strand in 1 M KCl. The transport of these constructs through single alpha-hemolysin pores was analysed by measuring the current blockade as a function of time. Complementary dsDNA takes significantly longer (840 +/- 60 micro s) to pass through the pore than a sequence of the same length containing a single (590 +/- 45 micro s) and a double (270 +/- 50 micro s) mismatch. Constructs involving three mismatches were indistinguishable from Guide ssDNA transport (120 +/- 30 micro s). The results suggest that dsDNA must unzip as it is transported through the nanopore. Duplexes containing mismatches unzip more quickly and can be distinguished from those with perfect complementarity.

Dielectrophoretic forces on the nanoscale

We have developed a method of calculation of the dielectrophoretic force on a nanoparticle in a fluid environment where variations in the electric field and electric field gradients are on the same nanoscale as the particle. The Boundary Element Dielectrophoretic Force (BEDF) method involves constructing a solvent-accessible or molecular surface surrounding the particle, calculating the normal component of the electric field at the surface boundary elements, and then solving a system of linear equations for the induced surface polarization charge on each element. Different surface elements of the molecule may experience quite different polarizing electric fields, unlike the situation in the point dipole approximation. A single 100-A-radius ring test configuration is employed to facilitate comparison with the well-known point dipole approximation (PDA). We find remarkable agreement between the forces calculated by the BEDF and PDA methods for a 1 A polarizable sphere. However, for larger particles, the differences between the methods become qualitative as well as quantitative; the character of the force changes from attractive at the origin of the ring for a 50-A sphere, to repulsive for a 75-A sphere. Equally dramatic differences are found in a more complex electrical environment involving two sets of 10 rings.

PROBING SINGLE DNA MOLECULE TRANSPORT USING FABRICATED NANOPORES

Nanopores can serve as high throughput, single molecule sensing devices that provide insight into the distribution of static and dynamic molecular activities, properties, or interactions. We have studied double stranded DNA electrophoretic transport dynamics through fabricated nanopores in silicon nitride. A fabricated pore enables us to interrogate a broader range of molecules with a wider range of conditions than can be investigated in a self-assembled protein pore in a lipid membrane.

Interaction of a polar molecule with an ion channel

The binding of a polar macromolecule to a large ion channel is studied theoretically, paying special attention to the influence of external conditions (applied voltage and ion strength of solution). The molecule behavior in bound state is considered as random thermal fluctuations within a limited fraction of its phase space. The mean duration of molecule binding (residence time tau r) is represented as the mean first passage time to reach the boundary of that restricted domain. By invoking the adiabatic approximation we reduce the problem to one dimension with the angle between macromolecule dipole and channel axes being the key variable of the problem. The model accounts for experimental measurements of tau r for the antibiotic Ampicillin within the bacterial porin OmpF of Escherichia coli. By assuming that the electrical interaction between Ampicillin dipole and OmpF ionizable groups affects the fluctuations, we find that the biased residence time-voltage dependence observed in experiments is the result of the strong transversal electric field in OmpF constriction with a tilt approximately 30 degrees aside the cis side.

Frequency and voltage dependence of the dielectrophoretic trapping of short lengths of DNA and dCTP in a nanopipette

The study of the properties of DNA under high electric fields is of both fundamental and practical interest. We have exploited the high electric fields produced locally in the tip of a nanopipette to probe the motion of double- and single-stranded 40-mer DNA, a 1-kb single-stranded DNA, and a single-nucleotide triphosphate (dCTP) just inside and outside the pipette tip at different frequencies and amplitudes of applied voltages. We used dual laser excitation and dual color detection to simultaneously follow two fluorophore-labeled DNA sequences with millisecond time resolution, significantly faster than studies to date. A strong trapping effect was observed during the negative half cycle for all DNA samples and also the dCTP. This effect was maximum below 1 Hz and decreased with higher frequency. We assign this trapping to strong dielectrophoresis due to the high electric field and electric field gradient in the pipette tip. Dielectrophoresis in electrodeless tapered nanostructures has potential applications for controlled mixing and manipulation of short lengths of DNA and other biomolecules, opening new possibilities in miniaturized biological analysis.

The Nanopore Electrode

The fabrication and electrochemical characterization of truncated cone-shaped nanopore electrodes are reported. A nanopore electrode is a Pt disk electrode embedded at the bottom of a conical pore, the circular orifice of the pore having nanometer dimensions. The electrochemical properties of nanopore electrodes with orifice radii of 39 and 74 nm are presented. Both the steady-state and transient voltammetric behavior of the nanopore electrode are reported and compared to predictions obtained using finite-element simulations. The truncated cone-shaped pore electrode possesses a unique transport property-the steady-state flux of molecules into a deep pore is limited by the restriction near the pore orifice, and thus, the steady-state current is independent of the pore depth. This characteristic is potentially useful in studying transport through nanometer-scale orifices.

Microscopic Kinetics of DNA Translocation through synthetic nanopores

We have previously demonstrated that a nanometer-diameter pore in a nanometer-thick metal-oxide-semiconductor-compatible membrane can be used as a molecular sensor for detecting DNA. The prospects for using this type of device for sequencing DNA are avidly being pursued. The key attribute of the sensor is the electric field-induced (voltage-driven) translocation of the DNA molecule in an electrolytic solution across the membrane through the nanopore. To complement ongoing experimental studies developing such pores and measuring signals in response to the presence of DNA, we conducted molecular dynamics simulations of DNA translocation through the nanopore. A typical simulated system included a patch of a silicon nitride membrane dividing water solution of potassium chloride into two compartments connected by the nanopore. External electrical fields induced capturing of the DNA molecules by the pore from the solution and subsequent translocation. Molecular dynamics simulations suggest that 20-basepair segments of double-stranded DNA can transit a nanopore of 2.2 x 2.6 nm(2) cross section in a few microseconds at typical electrical fields. Hydrophobic interactions between DNA bases and the pore surface can slow down translocation of single-stranded DNA and might favor unzipping of double-stranded DNA inside the pore. DNA occluding the pore mouth blocks the electrolytic current through the pore; these current blockades were found to have the same magnitude as the blockade observed when DNA transits the pore. The feasibility of using molecular dynamics simulations to relate the level of the blocked ionic current to the sequence of DNA was investigated.

Sizing DNA using a nanometer-diameter pore

Each species from bacteria to human has a distinct genetic fingerprint. Therefore, a mechanism that detects a single molecule of DNA represents the ultimate analytical tool. As a first step in the development of such a tool, we have explored using a nanometer-diameter pore, sputtered in a nanometer-thick inorganic membrane with a tightly focused electron beam, as a transducer that detects single molecules of DNA and produces an electrical signature of the structure. When an electric field is applied across the membrane, a DNA molecule immersed in electrolyte is attracted to the pore, blocks the current through it, and eventually translocates across the membrane as verified unequivocally by gel electrophoresis. The relationship between DNA translocation and blocking current has been established through molecular dynamics simulations. By measuring the duration and magnitude of the blocking current transient, we can discriminate single-stranded from double-stranded DNA and resolve the length of the polymer.

Nucleic acid transport through carbon nanotube membranes

We study the electrophoretic transport of single-stranded RNA molecules through 1.5-nm-wide pores of carbon nanotube membranes by molecular dynamics simulations. From approximately 170 individual RNA translocation events analyzed at full atomic resolution of solvent, membrane, and RNA, we identify key factors in membrane transport of biopolymers. RNA entry into the nanotube pores is controlled by conformational dynamics, and exit by hydrophobic attachment of RNA bases to the pores. Without electric field, RNA remains hydrophobically trapped in the membrane despite large entropic and energetic penalties for confining charged polymers inside nonpolar pores. Differences in RNA conformational flexibility and hydrophobicity result in sequence-dependent rates of translocation, a prerequisite for nanoscale separation devices.

Residue ionization and ion transport through OmpF channels

Single trimeric channels of the general bacterial porin, OmpF, were reconstituted into planar lipid membranes and their conductance, selectivity, and open-channel noise were studied over a wide range of proton concentrations. From pH 1 to pH 12, channel transport properties displayed three characteristic regimes. First, in acidic solutions, channel conductance is a strong function of pH; it increases by approximately threefold as the proton concentration decreases from pH 1 to pH 5. This rise in conductance is accompanied by a sharp increase in cation transport number and by pronounced open-channel low-frequency current noise with a peak at approximately pH 2.5. Random stepwise transients with amplitudes at approximately 1/5 of the monomer conductance are major contributors to this noise. Second, over the middle range (pH 5/pH 9), channel conductance and selectivity stay virtually constant; open channel noise is at its minimum. Third, over the basic range (pH 9/pH 12), channel conductance and cation selectivity start to grow again with an onset of a higher frequency open-channel noise. We attribute these effects to the reversible protonation of channel residues whose pH-dependent charge influences transport by direct interactions with ions passing through the channel.

Surface-charge-governed ion transport in nanofluidic channels

A study of ion transport in aqueous-filled silica channels as thin as 70 nm reveals a remarkable degree of conduction at low salt concentrations that departs strongly from bulk behavior: In the dilute limit, the electrical conductances of channels saturate at a value that is independent of both the salt concentration and the channel height. Our data are well described by an electrokinetic model parametrized only by the surface-charge density. Using chemical surface modifications, we further demonstrate that at low salt concentrations, ion transport in nanochannels is governed by the surface charge.

A nanosensor for transmembrane capture and identification of single nucleic Acid molecules

We have engineered a nanosensor for sequence-specific detection of single nucleic acid molecules across a lipid bilayer. The sensor is composed of a protein channel nanopore (alpha-hemolysin) housing a DNA probe with an avidin anchor at the 5' end and a nucleotide sequence designed to noncovalently bind a specific single-stranded oligonucleotide at the 3' end. The 3' end of the DNA probe is driven to the opposite side of the pore by an applied electric potential, where it can specifically bind to oligonucleotides. Reversal of the applied potential withdraws the probe from the pore, dissociating it from a bound oligonucleotide. The time required for dissociation of the probe-oligonucleotide duplex under this force yields identifying characteristics of the oligonucleotide. We demonstrate transmembrane detection of individual oligonucleotides, discriminate between molecules differing by a single nucleotide, and investigate the relationship between dissociation time and hybridization energy of the probe and analyte molecules. The detection method presented in this article is a candidate for in vivo single-molecule detection and, through parallelization in a synthetic device, for genotyping and global transcription profiling from small samples.

Atomic Layer Deposition to Fine-Tune the Surface Properties and Diameters of Fabricated Nanopores

Atomic layer deposition of alumina enhanced the molecule sensing characteristics of fabricated nanopores by fine-tuning their surface properties, reducing 1/f noise, neutralizing surface charge to favor capture of DNA and other negative polyelectrolytes, and controlling the diameter and aspect ratio of the pores with near single Ångstrom precision. The control over the chemical and physical nature of the pore surface provided by atomic layer deposition produced a higher yield of functional nanopore detectors.

DNA transport into Bacillus subtilis requires proton motive force to generate large molecular forces

Bacteria can acquire genetic diversity, including antibiotic resistance and virulence traits, by horizontal gene transfer. In particular, many bacteria are naturally competent for uptake of naked DNA from the environment in a process called transformation. Here, we used optical tweezers to demonstrate that the DNA transport machinery in Bacillus subtilis is a force-generating motor. Single DNA molecules were processively transported in a linear fashion without observable pausing events. Uncouplers inhibited DNA uptake immediately, suggesting that the transmembrane proton motive force is needed for DNA translocation. We found an uptake rate of 80 +/- 10 bp s(-1) that was force-independent at external forces <40 pN, indicating that a powerful molecular machine supports DNA transport.