Ion-beam sculpting at nanometre length scales

Polymer translocation through a nanopore under an applied external field

We investigate the dynamics of polymer translocation through a nanopore under an externally applied field using the two-dimensional fluctuating bond model with single-segment Monte Carlo moves. We concentrate on the influence of the field strength E, length of the chain N, and length of the pore L on forced translocation. As our main result, we find a crossover scaling for the translocation time tau with the chain length from tau approximately N2nu for relatively short polymers to tau approximately N1+nu for longer chains, where nu is the Flory exponent. We demonstrate that this crossover is due to the change in the dependence of the translocation velocity v on the chain length. For relatively short chains v approximately N-nu, which crosses over to v approximately N(-1) for long polymers. The reason for this is that with increasing N there is a high density of segments near the exit of the pore, which slows down the translocation process due to slow relaxation of the chain. For the case of a long nanopore for which R parallel, the radius of gyration Rg along the pore, is smaller than the pore length, we find no clear scaling of the translocation time with the chain length. For large N, however, the asymptotic scaling tau approximately N1+nu is recovered. In this regime, tau is almost independent of L. We have previously found that for a polymer, which is initially placed in the middle of the pore, there is a minimum in the escape time for R parallel approximately L. We show here that this minimum persists for weak fields E such that EL is less than some critical value, but vanishes for large values of EL.

Langevin dynamics simulations of ds-DNA translocation through synthetic nanopores

We have implemented a coarse-grained model to study voltage-driven as-DNA translocation through nanopores located in synthetic membranes. The simulated trajectory of the DNA through the nanopores was calculated using Langevin dynamics. We present the results based on more than 120,000 individual translocations. We are particularly interested in this work in probing the physical basis of various experimentally observed--yet poorly understood--phenomena. Notably, we observe in our simulations the formation of ds-DNA hairpins, widely suspected to be the basis for quantized blockage. We study the translocation time, a measurable quantity crucially important in polyelectrolyte characterization, as a function of hairpin vertex location along the polymer backbone, finding that this behavior can be tuned to some degree by simulation parameters. We also study the voltage dependence of the tendency of hairpins to serve as the initiators of translocation events. Surprisingly, we find that the resulting probability depends vitally upon whether the events counted are ultimately successful or not. Further details lead us to propose that failed attempts in experimental translocation studies may be more common--and deceptive--than is generally recognized. We find the time taken by successful single file translocations to be directly proportional to the ratio of chain length to the applied voltage. Finally, we address a common yet puzzling phenomenon in translocation experiments: translocation events in which the current through the pore is highly, yet incompletely, blocked. We present the findings that offer a new explanation for such events.

Driven polymer transport through a nanopore controlled by a rotating electric field: off-lattice computer simulations

The driven translocation kinetics of a single strand polynucleotide chain through a nanopore is studied using off-lattice Monte Carlo simulations, by which the authors demonstrate a novel method in controlling the driven polymer transport through a nanopore by a rotating electric field. The recorded time series of blockade current from the driven polynucleotide transport are used to determine the sequence of polynucleotides by implementing a modified Monte Carlo algorithm, in which the energy landscape paving technique is incorporated to avoid trapping at deep local minima. It is found that only six-time series of block current are required to completely determine the polynucleotide sequence if the average missing rate (AMR) of current signals in these time series is smaller than 20%. For those time series with AMR greater than 20%, the error rate in sequencing an unknown polynucleotide decreases rapidly by increasing the number of time series. To find the most appropriate experimental conditions, the authors have investigated the dependence of AMR of current signals and qualified rate of measured time series of blockade current on various controllable experimental variables.

Heteropolymer translocation through nanopores

The authors investigate the translocation dynamics of heteropolymers driven through a nanopore using a constant temperature Langevin thermostat. Specifically, they consider heteropolymers consisting of two types of monomers labeled A and B, which are distinguished by the magnitude of the driving force that they experience inside the pore. From a series of studies on polymers with sequences AmBn the authors identify both universal as well as specific sequence properties of the translocating chains. They find that the scaling of the average translocation time as a function of the chain length N remains unaffected by the heterogeneity, while the residence time of each bead is a strong function of the sequence for short repeat units. They further discover that for a symmetric heteropolymer AnBn of fixed length, the pattern exhibited by the residence times of the individual monomers has striking similarity with a double slit interference pattern where the total number of repeat units N/2n controls the number of interference fringes. These results are relevant for designing nanopore based sequencing techniques.

Effect of salt concentration on the electrophoretic speed of a polyelectrolyte through a nanopore

In a previous paper [S. Ghosal, Phys. Rev. E 74, 041901 (2006)] a hydrodynamic model for determining the electrophoretic speed of a polyelectrolyte through an axially symmetric slowly varying nanopore was presented in the limit of a vanishingly small Debye length. Here the case of a finite Debye layer thickness is considered while restricting the pore geometry to that of a cylinder of length much larger than the diameter. Further, the possibility of a uniform surface charge on the walls of the nanopore is taken into account. It is thereby shown that the calculated transit times are consistent with recent measurements in silicon nanopores.

Nanopore sensor for fast label-free detection of short double-stranded DNAs

Functionalizing surface enhanced the molecular sensing ability of a fabricated nanopore by increasing the translocation duration time for a short double-stranded DNA. The surface of nanopore was derivatized with gamma-aminopropyltriethoxysilane and the positively charged surface attracted DNA molecules when they were in the vicinity of nanopore. The translocation duration time of DNA increased due to the strong electrostatic interaction and it enabled us to detect a short double-stranded DNA (<1 kbp) that is under the size limit of a conventional solid state nanopore sensor. Both 539 and 910 bp double-stranded DNAs were analyzed with the surface functionalized nanopore and their translocation kinetics are presented in this work. The new feature of the surface modified nanopore that can detect short double-stranded DNA molecules could readily be applied for a rapid label-free diagnostic analysis in a Lab-On-a-Chip type DNA sensor.

Polymer translocation through a nanopore under a pulling force

We investigate polymer translocation through a nanopore under a pulling force using Langevin dynamics simulations. We concentrate on the influence of the chain length N and the pulling force F on the translocation time tau . The distribution of tau is symmetric and narrow for strong F . We find that tau approximately N{2} and translocation velocity v approximately N{-1} for both moderate and strong F . For infinitely wide pores, three regimes are observed for tau as a function of F . With increasing F , tau is independent of F for weak F , and then tau approximately F{-2+nu{-1}} for moderate F, where nu is the Flory exponent, which finally crosses over to tau approximately F{-1} for strong force. For narrow pores, even for moderate force tau approximately F{-1}. Finally, the waiting time, for monomer s and monomer s+1 to exit the pore, has a maximum for s close to the end of the chain, in contrast to the case where the polymer is driven by an external force within the pore.

Single-molecule mass spectrometry in solution using a solitary nanopore

We introduce a two-dimensional method for mass spectrometry in solution that is based on the interaction between a nanometer-scale pore and analytes. As an example, poly(ethylene glycol) molecules that enter a single alpha-hemolysin pore cause distinct mass-dependent conductance states with characteristic mean residence times. The conductance-based mass spectrum clearly resolves the repeat unit of ethylene glycol, and the mean residence time increases monotonically with the poly(ethylene glycol) mass. This technique could prove useful for the real-time characterization of molecules in solution.

Single molecule transcription profiling with AFM

Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.

Asymmetric properties of ion transport in a charged conical nanopore

Recently, the experimentally observed asymmetric properties of ion transport in charged conical nanopores (CCNs) that resemble those in biological ion channels have attracted a lot of attention in theoretical studies in nanotechnology research. In this paper, we report several tactics to study this effect by directly solving the Poisson-Nernst-Planck (PNP) equations. The result shows that PNP equations can indeed quantitatively describe the properties of these nanopores. Based on our numerical solutions, we contribute the rectification effect to ion-enrichment and ion-depletion. A detailed study of length dependence of current indicates that a relatively long length is indispensable for the CCNs to have rectification effect. We suggest that PNP equations and the calculation method could be further used to study other shapes of nanopores.

Sub-10 nm device fabrication in a transmission electron microscope

We show that a high-resolution transmission electron microscope can be used to fabricate metal nanostructures and devices on insulating membranes by nanosculpting metal films. Fabricated devices include nanogaps, nanodiscs, nanorings, nanochannels, and nanowires with tailored curvatures and multi-terminal nanogap devices with nanoislands or nanoholes between the terminals. The high resolution, geometrical flexibility, and yield make this fabrication method attractive for many applications including nanoelectronics and nanofluidics.

Polymer capture by electro-osmotic flow of oppositely charged nanopores

The authors have addressed theoretically the hydrodynamic effect on the translocation of DNA through nanopores. They consider the cases of nanopore surface charge being opposite to the charge of the translocating polymer. The authors show that, because of the high electric field across the nanopore in DNA translocation experiments, electro-osmotic flow is able to create an absorbing region comparable to the size of the polymer around the nanopore. Within this capturing region, the velocity gradient of the fluid flow is high enough for the polymer to undergo coil-stretch transition. The stretched conformation reduces the entropic barrier of translocation. The diffusion limited translocation rate is found to be proportional to the applied voltage. In the authors' theory, many experimental variables (electric field, surface potential, pore radius, dielectric constant, temperature, and salt concentration) appear through a single universal parameter. They have made quantitative predictions on the size of the adsorption region near the pore for the polymer and on the rate of translocation.

Unfolding of proteins and long transient conformations detected by single nanopore recording

We study the electrophoretic blockades due to entries of partially unfolded proteins into a nanopore as a function of the concentration of the denaturing agent. Short and long pore blockades are observed by electrical detection. Short blockades are due to the passage of completely unfolded proteins, their frequency increases as the concentration of the denaturing agent increases, following a sigmoidal denaturation curve. Long blockades reveal partially folded conformations. Their duration increases as the proteins are more folded. The observation of a Vogel-Fulcher law suggests a glassy behavior.

Fabrication of self-sealed circular nano/microfluidic channels in glass substrates

We realized self-sealing fluidics channels with circular cross-sections having diameters ranging between 30 and 2000 nm on a 200 mm glass wafer through CMOS compatible processes. Lateral voids were narrowed and sealed with non-conformal plasma enhanced chemical vapour deposition (PECVD) of phospho silicate glass (PSG) along silicon oxide trenches on silicon wafers. Leveraging on the reflow properties of PSG, circular profiled-channels were formed after undergoing high temperature annealing. These devices were subsequently transferred onto a borosilicate glass substrate through anodic bonding, and a fully transparent microfluidic device was achieved with the complete removal of the handle silicon substrate. The process offers a means of integrating electrochemical and optical sensing on the same platform, for biological research.

Solid-state nanopores

The passage of individual molecules through nanosized pores in membranes is central to many processes in biology. Previously, experiments have been restricted to naturally occurring nanopores, but advances in technology now allow artificial solid-state nanopores to be fabricated in insulating membranes. By monitoring ion currents and forces as molecules pass through a solid-state nanopore, it is possible to investigate a wide range of phenomena involving DNA, RNA and proteins. The solid-state nanopore proves to be a surprisingly versatile new single-molecule tool for biophysics and biotechnology.

Solid-state nanopore channels with DNA selectivity

Solid-state nanopores have emerged as possible candidates for next-generation DNA sequencing devices. In such a device, the DNA sequence would be determined by measuring how the forces on the DNA molecules, and also the ion currents through the nanopore, change as the molecules pass through the nanopore. Unlike their biological counterparts, solid-state nanopores have the advantage that they can withstand a wide range of analyte solutions and environments. Here we report solid-state nanopore channels that are selective towards single-stranded DNA (ssDNA). Nanopores functionalized with a 'probe' of hair-pin loop DNA can, under an applied electrical field, selectively transport short lengths of 'target' ssDNA that are complementary to the probe. Even a single base mismatch between the probe and the target results in longer translocation pulses and a significantly reduced number of translocation events. Our single-molecule measurements allow us to measure separately the molecular flux and the pulse duration, providing a tool to gain fundamental insight into the channel-molecule interactions. The results can be explained in the conceptual framework of diffusive molecular transport with particle-channel interactions.

Nanopore sequencing technology: nanopore preparations

For the past decade, nanometer-scale pores have been developed as a powerful technique for sensing biological macromolecules. Various potential applications using these nanopores have been reported at the proof-of-principle stage, with the eventual aim of using them as an alternative to de novo DNA sequencing. Currently, there have been two general approaches to prepare nanopores for nucleic acid analysis: organic nanopores, such as alpha-hemolysin pores, are commonly used for DNA analysis, whereas synthetic solid-state nanopores have also been developed using various conventional and non-conventional fabrication techniques. In particular, synthetic nanopores with pore sizes smaller than the alpha-hemolysin pores have been prepared, primarily by electron-beam-assisted techniques: these are more robust and have better dimensional adjustability. This review will examine current methods of nanopore preparation, ranging from organic pore preparations to recent developments in synthetic nanopore fabrications.

The effect of translocating cylindrical particles on the ionic current through a nanopore

The electric field-induced translocation of cylindrical particles through nanopores with circular cross sections is studied theoretically. The coupled Nernst-Planck equations (multi-ion model, MIM) for the concentration fields of the ions in solution and the Stokes equation for the flow field are solved simultaneously. The predictions of the multi-ion model are compared with the predictions of two simplified models based on the Poisson-Boltzmann equation (PBM) and the Smoluchowski's slip velocity (SVM). The concentration field, the ionic current though the pore, and the particle's velocity are computed as functions of the particle's size, location, and electric charge; the pore's size and electric charge; the electric field intensity; and the bulk solution's concentration. In qualitative agreement with experimental data, the MIM predicts that, depending on the bulk solution's concentration, the translocating particle may either block or enhance the ionic current. When the thickness of the electric double layer is relatively large, the PBM and SVM predictions do not agree with the MIM predictions. The limitations of the PBM and SVM are delineated. The theoretical predictions are compared with and used to explain experimental data pertaining to the translocation of DNA molecules through nanopores.

Threading synthetic polyelectrolytes through protein pores

We have measured the ionic current signatures of sodium poly(styrene sulfonate) as its single molecules translocate through an alpha-hemolysin pore embedded into a bilayer in a salty aqueous medium under an externally applied electric field. As in the previous experiments involving DNA and RNA, the pore current, which is a measure of the ionic conductivity of the low molar mass electrolyte ions, is significantly reduced when the polymer molecule translocates through the pore. The magnitude and the duration of the reduction in the pore current are measured for each of the translocation events. By studying thousands of events of reduction in the ionic current, we have constructed distribution functions for the extent of the reduced current and for the translocation time. The details of these distribution functions are significantly different from those for DNA and RNA. By investigating over two orders of magnitude in the molecular weight of the polymer, the average translocation time is found to be proportional to the molecular weight and inversely proportional to the applied voltage. This demonstration of threading a synthetic polyelectrolyte through a protein pore opens up many opportunities to systematically explore the fundamental physical principles behind translocation of single macromolecules, by resorting to the wide variety of synthetically available polymers without the complexities arising from the sequences of biological polymers. In addition, the present experiments suggest yet another experimental protocol for separation of polymer molecules directly in aqueous media.

Fabricating nanofluidic channels and Applying it for single bio-molecule study

In the emerging field of nanobiotechnology, further downsizing the fluidic channels to the nanometer scale is attractive for both fundamental studies and technical applications. The insulation Silicon nitride membrane nanofluidic channel array which have width&#8764;75nm and depth &#8764; 100nm and length 50&#956;m were created by focused-ion- beam instrument, the&#955;--DNA molecules were put inside them and the dynamic characteristics were initial studied, a fluorescence microscopy was used to observe the images. We observed &#955;--DNA moved inside the nanotrenches which dealt with activating reagent Brij aqueous solution only by capillary force,this will help us to understand more DNA dynamics characteristics and more information about single biomolecule transporting through a nanopore,.

Biological sensing with an on-chip resistive pulse analyzer

Resistive pulse sensors (or Coulter counters) detect the conductance change caused by single fluid-borne particles transiting a pore. Their simplicity in design and use, along with their capability for single-molecule sensitivity, make them well-suited to the analysis of biological particles. Here, we use standard methods of micro- and nanolithography to construct resistive-pulse devices that combine microfluidics with electronic sensing. We use the devices to detect single latex colloids, single DNA molecules, and specific antibody/antigen binding. We discuss the advantages of our design, and prospects for future applications.

Effective charge and free energy of DNA inside an ion channel

Translocation of a single stranded DNA (ssDNA) through an alpha -hemolysin channel in a lipid membrane driven by applied transmembrane voltage V was extensively studied recently. While the bare charge of the ssDNA piece inside the channel is approximately 12 (in units of electron charge) measurements of different effective charges resulted in values between one and two. We explain these challenging observations by a large self-energy of a charge in the narrow water filled gap between ssDNA and channel walls, related to large difference between dielectric constants of water and lipid, and calculate effective charges of ssDNA. We start from the most fundamental stall charge q(s), which determines the force F(s)=q(s)V/L stalling DNA against the voltage V ( L is the length of the channel). We show that the stall charge q(s) is proportional to the ion current blocked by DNA, which is small due to the self-energy barrier. Large voltage V reduces the capture barrier which DNA molecule should overcome in order to enter the channel by /q(c)/V, where q(c) is the effective capture charge. We expressed it through the stall charge q(s). We also relate the stall charge q(s) to two other effective charges measured for ssDNA with a hairpin in the back end: the charge q(u) responsible for reduction of the barrier for unzipping of the hairpin and the charge q(e) responsible for DNA escape in the direction of hairpin against the voltage. At small V we explain reduction of the capture barrier with the salt concentration.

Surface damage induced by FIB milling and imaging of biological samples is controllable

Focused ion beam (FIB) techniques are among the most important tools for the nanostructuring of surfaces. We used the FIB/SEM (scanning electron microscope) for milling and imaging of digestive gland cells. The aim of our study was to document the interactions of FIB with the surface of the biological sample during FIB investigation, to identify the classes of artifacts, and to test procedures that could induce the quality of FIB milled sections by reducing the artifacts. The digestive gland cells were prepared for conventional SEM. During FIB/SEM operation we induced and enhanced artifacts. The results show that FIB operation on biological tissue affected the area of the sample where ion beam was rastering. We describe the FIB-induced surface major artifacts as a melting-like effect, sweating-like effect, morphological deformations, and gallium (Ga(+)) implantation. The FIB induced surface artifacts caused by incident Ga(+) ions were reduced by the application of a protective platinum strip on the surface exposed to the beam and by a suitable selection of operation protocol. We recommend the same sample preparation methods, FIB protocol for milling and imaging to be used also for other biological samples.

Developing synthetic conical nanopores for biosensing applications

In this review we bring together recent results from our group focused towards the development of biosensors from single conically-shaped artificial nanopores. The nanopores, used in the work presented here, were prepared using the track-etch process. The fabrication of track-etched conical nanopores has been optimized to allow for single nanopores with reproducible dimensions to be prepared. We have also demonstrated techniques that allow for easy and controllable manipulation of nanopore geometry (e.g., cone angle). We will consider the ion transport properties of the conical nanopores and factors that affect these properties. Methods for introducing functions that mimic biological ion channels, such as voltage-gating, into these nanopores will also be addressed. Three prototype sensors developed from single conical nanopores will be presented. In the first two sensors, the single conical nanopores function as resistive-pulse sensors and detect the presence of analytes as current-blockade events in the ion current. The third sensor functions in an on/off mode, much like a ligand-gated ion channel. In the presence of a target analyte, the ion current permanently shuts off.

Electrically tunable solid-state silicon nanopore ion filter

We show that a nanopore in a silicon membrane connected to a voltage source can be used as an electrically tunable ion filter. By applying a voltage between the heavily doped semiconductor and the electrolyte, it is possible to invert the ion population inside the nanopore and vary the conductance for both cations and anions in order to achieve selective conduction of ions even in the presence of significant surface charges in the membrane. Our model based on the solution of the Poisson equation and linear transport theory indicates that in narrow nanopores substantial gain can be achieved by controlling electrically the width of the charge double layer.

Focused ion beam induced deflections of freestanding thin films

Prominent deflections are shown to occur in freestanding silicon nitride thin membranes when exposed to a 50 keV gallium focused ion beam for ion doses between 10(14) and 10(17) ions/cm(2). Atomic force microscope topographs were used to quantify elevations on the irradiated side and corresponding depressions of comparable magnitude on the back side, thus indicating that what at first appeared to be protrusions are actually the result of membrane deflections. The shape in high-stress silicon nitride is remarkably flattopped and differs from that in low-stress silicon nitride. Ion beam induced biaxial compressive stress generation, which is a known deformation mechanism for other amorphous materials at higher ion energies, is hypothesized to be the origin of the deflection. A continuum mechanical model based on this assumption convincingly reproduces the profiles for both low-stress and high-stress membranes and provides a family of unusual shapes that can be created by deflection of freestanding thin films under beam irradiation.

DNA counterion current and saturation examined by a MEMS-based solid state nanopore sensor

Reports of DNA translocation measurements have been increasing rapidly in recent years due to advancements in pore fabrication and these measurements continue to provide insight into the physics of DNA translocations through MEMS based solid state nanopores. Specifically, it has recently been demonstrated that in addition to typically observed current blockages, enhancements in current can also be measured under certain conditions. Here, we further demonstrate the power of these nanopores for examining single DNA molecules by measuring these ionic currents as a function of the applied electric field and show that the direction of the resulting current pulse can provide fundamental insight into the physics of condensed counterions and the dipole saturation in single DNA molecules. Expanding on earlier work by Manning and others, we propose a model of DNA counterion ionic current and saturation of this current based on our experimental results. The work can have broad impact in understanding DNA sensing, DNA delivery into cells, DNA conductivity, and molecular electronics.

Pressure-driven transport of confined DNA polymers in fluidic channels

The pressure-driven transport of individual DNA molecules in 175-nm to 3.8-microm high silica channels was studied by fluorescence microscopy. Two distinct transport regimes were observed. The pressure-driven mobility of DNA increased with molecular length in channels higher than a few times the molecular radius of gyration, whereas DNA mobility was practically independent of molecular length in thin channels. In addition, both the Taylor dispersion and the self-diffusion of DNA molecules decreased significantly in confined channels in accordance with scaling relationships. These transport properties, which reflect the statistical nature of DNA polymer coils, may be of interest in the development of "lab-on-a-chip" technologies.

What is the future of electrophoresis in large-scale genomic sequencing?

Although a finished human genome reference sequence is now available, the ability to sequence large, complex genomes remains critically important for researchers in the biological sciences, and in particular, continued human genomic sequence determination will ultimately help to realize the promise of medical care tailored to an individual's unique genetic identity. Many new technologies are being developed to decrease the costs and to dramatically increase the data acquisition rate of such sequencing projects. These new sequencing approaches include Sanger reaction-based technologies that have electrophoresis as the final separation step as well as those that use completely novel, nonelectrophoretic methods to generate sequence data. In this review, we discuss the various advances in sequencing technologies and evaluate the current limitations of novel methods that currently preclude their complete acceptance in large-scale sequencing projects. Our primary goal is to analyze and predict the continuing role of electrophoresis in large-scale DNA sequencing, both in the near and longer term.

Nanopore Detector based analysis of single-molecule conformational kinetics and binding interactions

Background

A Nanopore Detector provides a means to transduce single molecule events into observable channel current changes. Nanopore-based detection can report directly, or indirectly, on single molecule kinetics. The nanopore-based detector can directly measure molecular characteristics in terms of the blockade properties of individual molecules – this is possible due to the kinetic information that is embedded in the blockade measurements, where the adsorption-desorption history of the molecule to the surrounding channel, and the configurational changes in the molecule itself, imprint on the ionic flow through the channel. This rich source of information offers prospects for DNA sequencing and single nucleotide polymorphism (SNP) analysis. A nanopore-based detector can also measure molecular characteristics indirectly, by using a reporter molecule that binds to certain molecules, with subsequent distinctive blockade by the bound-molecule complex.

Results

It is hypothesized that reaction histories of individual molecules can be observed on model DNA/DNA, DNA/Protein, and Protein/Protein systems. Preliminary results are all consistent with this hypothesis. Nanopore detection capabilities are also described for highly discriminatory biosensing, binding strength characterization, and rapid immunological screening.

Conclusion

In essence, the heart of chemistry is now accessible to a new, single-molecule, observation method that can track both external molecular binding states, and internal conformation states.

Nanobubbles in solid-state nanopores

From conductance and noise studies, we infer that nanometer-sized gaseous bubbles (nanobubbles) are the dominant noise source in solid-state nanopores. We study the ionic conductance through solid-state nanopores as they are moved through the focus of an infrared laser beam. The resulting conductance profiles show strong variations in both the magnitude of the conductance and in the low-frequency noise when a single nanopore is measured multiple times. Differences up to 5 orders of magnitude are found in the current power spectral density. In addition, we measure an unexpected double-peak ionic conductance profile. A simple model of a cylindrical nanopore that contains a nanobubble explains the measured profile and accounts for the observed variations in the magnitude of the conductance.

Estimation of solid phase affinity constants using resistive-pulses from functionalized nanoparticles

This paper describes a method for estimating the solid phase affinity constant of antibodies by using resistive-pulse (Coulter counting) data from spherical nanoparticles that expose antigens. We developed this technique by analyzing data published recently by Saleh, O.A., Sohn, L.L., 2003a. Proc. Natl. Acad. Sci. U.S.A. 100, 820-824. These authors used resistive-pulse sensing to detect an increase in the diameter of streptavidin-functionalized colloids due to the binding of monoclonal anti-streptavidin antibodies. Based on further analysis of their data, we were able to determine the number of antibodies bound to the colloids at various antibody concentrations. This information made it possible to estimate the solid phase affinity constant of the interaction by fitting the data with binding isotherms that describe the binding equilibrium between antibody and antigen. We calculated a value of 2.6x10(8)+/-0.8x10(8) M-1 which is in agreement with the specifications of the supplier of the antibody.

Conformational analysis of single DNA molecules undergoing entropically induced motion in nanochannels

We have used the interface between a nanochannel and a microchannel as a tool for applying controlled forces on a DNA molecule. A molecule, with a radius of gyration larger than the nanochannel width, that straddles such an interface is subject to an essentially constant entropic force, which can be balanced against other forces such as the electrophoretic force from an applied electric field. By controlling the applied field we can position the molecule as desired and observe the conformation of the molecule as it stretches, relaxes, and recoils from the nanochannel. We quantify and present models for the molecular motion in response to the entropic, electrophoretic, and frictional forces acting on it. By determining the magnitude of the drag coefficients for DNA molecules in the nanostructure, we are able to estimate the confinement-induced recoil force. Finally, we demonstrate that we can use a controlled applied field and the entropic interfacial forces to unfold molecules, which can then be manipulated and positioned in their simple extended morphology.

Microfabricated nanochannel implantable drug delivery devices: trends, limitations and possibilities

This is a review of the application of microfabrication technologies, borrowed from the semiconductor industry, to drug delivery implants incorporating structures in the nanometer dimension. In the futuristic ideal, these systems would involve the implantation of precisely microfabricated drug delivery systems with nanopores, nanochannels and/or nanoreservoirs fabricated from silicon, coupled with electronic sensing and actuator systems, for the precise, timed and/or targeted delivery of drugs. After more than a decade in conceptualisation and experimentation, four systems that have commercial potential are discussed: i) implantable microchips with on-demand microdosage for one or more therapeutic agents under internal control or external control using a wireless link; ii) nanopore pumps, implantable titanium pumps, consisting of a drug reservoir with a nanopore-release membrane, capable of delivering potent small or macromolecules at constant serum levels for sustained periods of time; iii) nanocages, microfabricated nanopore immunoisolation chambers for cellular implants, capable of natural feedback-controlled delivery of proteins and peptides; and iv) nanobuckets, micromachined silicon porous particles with drug-loading capacity and targeting ligands for localised delivery. Each of the systems, along with future trends in microfabrication manufacturing, limitations and possibilities, are discussed.

Influence of electric field intensity, ionic strength, and migration distance on the mobility and diffusion in DNA surface electrophoresis

In order to increase the separation rate of surface electrophoresis while preserving the resolution for large DNA chains, e.g., genomic DNA, the mobility and diffusion of Lambda DNA chains adsorbed on flat silicon substrate under an applied electric field, as a function of migration distance, ionic strength, and field intensity, were studied using laser fluorescence microscope. The mobility was found to follow a power law with the field intensity beyond a certain threshold. The detected DNA peak width was shown to be constant with migration distance, slightly smaller with stronger field intensity, but significantly decreased with higher ionic strength. The molecular dynamics simulation demonstrated that the peak width was strongly related with the conformation of DNA chains adsorbed onto surface. The results also implied that there was no diffusion of DNA during migration on surface. Therefore, the Nernst-Einstein relation is not valid in the surface electrophoresis and the separation rate could be improved without losing resolution by decreasing separation distance, increasing buffer concentration, and field intensity. The results indicate the fast separation of genomic DNA chains by surface electrophoresis is possible.

Eddies in a bottleneck: an arbitrary Debye length theory for capillary electroosmosis

Using an applied electrical field to drive fluid flows becomes desirable as channels become smaller. Although most discussions of electroosmosis treat the case of thin Debye layers, here electroosmotic flow (EOF) through a constricted cylinder is presented for arbitrary Debye lengths (kappa(-1)) using a long wavelength perturbation of the cylinder radius. The analysis uses the approximation of small potentials. The varying diameter of the cylinder produces radially and axially varying effective electric fields, as well as an induced pressure gradient. We predict the existence of eddies for certain constricted geometries and propose the possibility of electrokinetic trapping in these regions. We also present a leading-order criterion which predicts central eddies in very narrow constrictions at the scale of the Debye length. Eddies can be found both in the center of the channel and along the perimeter, and the presence of the eddies is a consequence of the induced pressure gradient that accompanies electrically driven flow into a narrow constriction.

Ion exchange phase transitions in water-filled channels with charged walls

Ion transport through narrow water-filled channels is impeded by a high electrostatic barrier. The latter originates from the large ratio of the dielectric constants of the water and the surrounding media. We show that "doping," i.e., immobile charges attached to the walls of the channel, substantially reduces the barrier. This explains why most of the biological ion channels are "doped." We show that at rather generic conditions the channels may undergo ion exchange phase transitions (typically of the first order). Upon such a transition a finite latent concentration of ions may either enter or leave the channel, or be exchanged between the ions of different valences. We discuss possible implications of these transitions for the Ca-vs-Na selectivity of biological Ca channels. We also show that transport of divalent Ca ions is assisted by their fractionalization into two separate excitations.

Fast DNA sequencing via transverse electronic transport

A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of single-stranded DNA while it translocates through a nanopore. Our estimates, based on the statistics of these distributions, reveal that sequencing of an entire human genome could be done with very high accuracy in a matter of hours without parallelization, that is, orders of magnitude faster than present techniques. The practical implementation of our approach would represent a substantial advancement in our ability to study, predict, and cure diseases from the perspective of the genetic makeup of each individual.

Isolating the step contribution to the uniaxial magnetic anisotropy in nanostructured Fe/Ag(001) films

We have investigated the possibility of isolating the step-induced in-plane uniaxial magnetic anisotropy in Fe/Ag(001) films on which nanoscale surface ripples were fabricated by the ion sculpting technique. For rippled Fe films deposited on flat Ag(001), the steps created along the ripple sidewalls are shown to be the only source of uniaxial anisotropy. Ion sculpting of ultrathin magnetic films allows one to selectively study the step-induced anisotropy and to investigate the correlation between local atomic environment and magnetic properties.

Nanoscale volcanoes: accretion of matter at ion-sculpted nanopores

We demonstrate the formation of nanoscale volcano-like structures induced by ion-beam irradiation of nanoscale pores in freestanding silicon nitride membranes. Accreted matter is delivered to the volcanoes from micrometer distances along the surface. Volcano formation accompanies nanopore shrinking and depends on geometrical factors and the presence of a conducting layer on the membrane's back surface. We argue that surface electric fields play an important role in accounting for the experimental observations.