Ion-beam sculpting at nanometre length scales

Theory of DNA translocation through narrow ion channels and nanopores with charged walls

Translocation of a single-stranded DNA molecule through genetically engineered alpha -hemolysin channels with positively charged walls is studied. It is predicted that transport properties of such channels are dramatically different from neutral wild-type alpha -hemolysin channels. We assume that the wall charges compensate a fraction x of the bare charge q_{b} of the DNA piece residing in the channel. Our predictions are as follows. (i) At small concentration of salt the blocked ion current decreases with x . (ii) The effective charge q_{s} of the DNA piece, which is very small at x=0 (neutral channel) grows with x and at x=1 reaches q_{b} . (iii) The rate of DNA capture by the channel grows exponentially with x . Our theory is also applicable to translocation of a double-stranded DNA molecular in narrow solid state nanopores with positively charged walls.

Nucleotide identification and orientation discrimination of DNA homopolymers immobilized in a protein nanopore

Nanopores have been used as extremely sensitive resistive pulse sensors to detect analytes at the molecular level. There has been interest in using such a scheme to rapidly and inexpensively sequence single molecules of DNA. To establish reference current levels for adenine, cytosine, and thymine nucleotides, we measured the blockage currents following immobilization of single-stranded DNA polyadenine, polycytosine, and polythymine within a protein nanopore in chemical orientations in which either the 3' or the 5' end enters the pore. Immobilization resulted in low-noise measurements, yielding sharply defined current distributions for each base that enabled clear discrimination of the nucleotides in both orientations. In addition, we find that not only is the blockage current for each polyhomonucleotide orientation dependent, but also the changes in orientation affect the blockage currents for each base differently. This dependence can affect the ability to resolve polyadenine and polythymine; with the 5' end entering the pore, the separation between polyadenine and polythymine is double that observed for the 3' orientation. This suggests that, for better resolution, DNA should be threaded through the 5' end first in nanopore DNA sequencing experiments.

DNA translocation governed by interactions with solid-state nanopores

We investigate the voltage-driven translocation dynamics of individual DNA molecules through solid-state nanopores in the diameter range 2.7-5 nm. Our studies reveal an order of magnitude increase in the translocation times when the pore diameter is decreased from 5 to 2.7 nm, and steep temperature dependence, nearly threefold larger than would be expected if the dynamics were governed by viscous drag. As previously predicted for an interaction-dominated translocation process, we observe exponential voltage dependence on translocation times. Mean translocation times scale with DNA length by two power laws: for short DNA molecules, in the range 150-3500 bp, we find an exponent of 1.40, whereas for longer molecules, an exponent of 2.28 dominates. Surprisingly, we find a transition in the fraction of ion current blocked by DNA, from a length-independent regime for short DNA molecules to a regime where the longer the DNA, the more current is blocked. Temperature dependence studies reveal that for increasing DNA lengths, additional interactions are responsible for the slower DNA dynamics. Our results can be rationalized by considering DNA/pore interactions as the predominant factor determining DNA translocation dynamics in small pores. These interactions markedly slow down the translocation rate, enabling higher temporal resolution than observed with larger pores. These findings shed light on the transport properties of DNA in small pores, relevant for future nanopore applications, such as DNA sequencing and genotyping.

Nanofluidic ionic diodes. Comparison of analytical and numerical solutions

Recently reported experimental and theoretical studies of nanofluidic nonlinear devices, such as bipolar and unipolar ionic diodes, have yet to answer the question about the possibility of their further miniaturization. In this Article, we theoretically investigate the effects of size reduction, applied bias, and solution ionic strength in such devices. We compare the numerical solutions of the Poisson, Nernst-Planck (PNP), and Navier-Stokes (NS) equations with their one-dimensional, analytical approximations. We demonstrate that the contribution of electroosmosis is insignificant and find analytical approximations to PNP for bipolar and unipolar diodes that are in good agreement with numerical 3D solutions. We identify the minimal dimensions for such diodes that demonstrate ion current rectification behavior and demonstrate the importance of the edge effect in very short diodes.

Fabrication of one-dimensional programmable-height nanostructures via dynamic stencil deposition

Dynamic stencil deposition (DSD) techniques offer a variety of fabrication advantages not possible with traditional lithographic processing, such as the ability to directly deposit nanostructures with programmable-height profiles. However, DSD systems have not enjoyed widespread usage due to their complexity. We demonstrate a simple, low-profile, portable, one-dimensional nanotranslation system that facilitates access to nanoscale DSD abilities. Furthermore we show a variety of fabricated programmable-height nanostructures, including parallel arrays of such structures, and suggest other applications that exploit the unique capabilities of DSD fabrication methods.

Controlled fabrication of nanopores using a direct focused ion beam approach with back face particle detection

We report a direct, ion drilling technique that enables the reproducible fabrication and placement of nanopores in membranes of different thickness. Using a 30 keV focused Ga ion beam column combined with an in situ, back face, multi-channelplate particle detector, nanopores are sputtered in Si(3)N(4) and W/Si(3)N(4) to have diameters as small as 12 nm. Transmission electron microscopy shows that focused ion beam-drilled holes are near-conical with the diameter decreasing from entry to exit side. By monitoring the detector signal during ion exposure, the drilled hole width can be minimized such that the exit-side diameter is smaller than the full width at half-maximum of the nominally Gaussian-shaped incident beam. Judicious choice of the beam defining aperture combined with back face particle detection allows for reproducible exit-side hole diameters between 18 and 100 nm. The nanopore direct drilling technique does not require potentially damaging broad area exposure to tailor hole sizes. Moreover, this technique successfully achieves breakthrough despite the effects of varying membrane thickness, redeposition, polycrystalline grain structure, and slight ion beam current fluctuations.

Gating of single synthetic nanopores by proton-driven DNA molecular motors

Switchable ion channels that are made of membrane proteins play different roles in cellular circuits. Since gating nanopore channels made of proteins can only work in the environment of lipid membrane, they are not fully compatible to the application requirement as a component of those nanodevice systems in which lipid membranes are hard to establish. Here we report a synthetic nanopore-DNA system where single solid-state conical nanopores can be reversibly gated by switching DNA motors immobilized inside the nanopores. High- (on-state) and low- (off-state) conductance states were found within this nanopore-DNA system corresponding to the single-stranded and i-motif structures of the attached DNA motors. The highest gating efficiency indicated as current ratio of on-state versus off-state was found when the length of the attached DNA molecule matched the tip diameter of the nanopore well. This novel nanopore-DNA system, which was gated by collective folding of structured DNA molecules responding to the external stimulus, provided an artificial counterpart of switchable protein-made nanopore channels. The concept of this DNA motor-driven nanopore switch can be used to build novel, biologically inspired nanopore machines with more precisely controlled functions in the near future by replacing the DNA molecules with other functional biomolecules, such as polypeptides or protein enzymes.

Subcutoff microwave driven plasma ion sources for multielemental focused ion beam systems

A compact microwave driven plasma ion source for focused ion beam applications has been developed. Several gas species have been experimented including argon, krypton, and hydrogen. The plasma, confined by a minimum B multicusp magnetic field, has good radial and axial uniformity. The octupole multicusp configuration shows a superior performance in terms of plasma density (~1.3 x 10(11) cm(-3)) and electron temperature (7-15 eV) at a power density of 5-10 Wcm(2). Ion current densities ranging from a few hundreds to over 1000 mA/cm(2) have been obtained with different plasma electrode apertures. The ion source will be combined with electrostatic Einzel lenses and should be capable of producing multielemental focused ion beams for nanostructuring and implantations. The initial simulation results for the focused beams have been presented.

Experimental characterization of a metal-oxide-semiconductor field-effect transistor-based Coulter counter

We report the detailed characterization of an ultrasensitive microfluidic device used to detect the translocation of small particles through a sensing microchannel. The device connects a fluidic circuit to the gate of a metal-oxide-semiconductor field-effect transistor (MOSFET) and detects particles by monitoring the MOSFET drain current modulation instead of the modulation in the ionic current through the sensing channel. The minimum volume ratio of the particle to the sensing channel detected is 0.006%, which is about ten times smaller than the lowest detected volume ratio previously reported in the literature. This volume ratio is detected at a noise level of about 0.6% of the baseline MOSFET drain current, clearly showing the amplification effects from the fluidic circuits and the MOSFETs. We characterize the device sensitivity as a function of the MOSFET gate potential and show that its sensitivity is higher when the MOSFET is operating below its threshold gate voltage than when it is operating above the threshold voltage. In addition, we demonstrate that the device sensitivity linearly increases with the applied electrical bias across the fluidic circuit. Finally, we show that polystyrene beads and glass beads with similar sizes can be distinguished from each other based on their different translocation times, and the size distribution of microbeads can be obtained with accuracy comparable to that of direct scanning electron microscopy measurements.

Ultrafast laser fabrication of submicrometer pores in borosilicate glass

We demonstrate rapid fabrication of submicrometer-diameter pores in borosilicate glass using femtosecond laser machining and subsequent wet-etch techniques. This approach allows direct and repeatable fabrication of high-quality pores with diameters of 400-800 nm. Such small pores coupled with the desirable electrical and chemical properties of glass enable sensitive resistive-pulse analysis to determine the size and concentration of macromolecules and nanoparticles. Plasma-enhanced chemical vapor deposition allows further reduction of pore diameters to below 300 nm.

Label-free detection of single protein molecules and protein-protein interactions using synthetic nanopores

Nanofabricated pores in 20 nm-thick silicon nitride membranes were used to probe various protein analytes as well as to perform an antigen-antibody binding assay. A two-compartment electrochemical cell was separated by a single nanopore, 28 nm in diameter. Adding proteins to one compartment caused current perturbations in the ion current flowing through the pore. These perturbations correlated with both the charge and the size of the protein or of a protein-protein complex. The potential of this nanotechnology for studying protein-protein interactions is highlighted with the sensitive detection of beta-human chorionic gonadotropin, a hormone and clinical biomarker of pregnancy, by monitoring in real time and at a molecular level the formation of a complex between hormones and antibodies in solution. In this form, the assay compared advantageously to immunoassays, with the important difference that labels, immobilization, or amplification steps were no longer needed. In conclusion, we present proof-of-principle that properties of proteins and their interactions can be investigated in solution using synthetic nanopores and that these interactions can be exploited to measure protein concentrations accurately.

Nanogap detector inside nanofluidic channel for fast real-time label-free DNA analysis

We report fabrication and characterization of a novel real-time, label-free DNA detector, that uses a long nanofluidic channel to stretch a DNA strand and a nanogap detector (with a gap as small as 9 nm) inside the channel to measure the electrical conduction perpendicular to the DNA backbone as it moves through the gap. We have observed electrical signals caused by 1.1 kilobase-pair (kbp) double-stranded (ds)-DNA passing through the gap in the nanogap detectors with a gap equal to or less than 13 nm.

Noise and bandwidth of current recordings from submicrometer pores and nanopores

Nanopores and submicrometer pores have recently been explored for applications ranging from detection of single molecules, assemblies of nanoparticles, nucleic acids, occurrence of chemical reactions, and unfolding of proteins. Most of these applications rely on monitoring electrical current through these pores, hence the noise and signal bandwidth of these current recordings are critical for achieving accurate and sensitive measurements. In this report, we present a detailed theoretical and experimental study on the noise and signal bandwidth of current recordings from glass and polyethylene terephthalate (PET) membranes that contain a single submicrometer pore or nanopore. We examined the theoretical signal bandwidth of two different pore geometries, and we measured the signal bandwidth of the electronics used to record the ionic current. We also investigated the theoretical noise generated by the substrate material, the pore, and the electronics used to record the current. Employing a combination of theory and experimental results, we were able to predict the noise in current traces recorded from glass and PET pores with no applied voltage with an error of less than 12% in a range of signal bandwidths from 1 to 40 kHz. In approximately half of all experiments, application of a voltage did not significantly increase the noise. In the other half of experiments, however, application of a voltage resulted in an additional source of noise. For these pores, predictions of the noise were usually still accurate within 35% error at signal bandwidths of at least 10 kHz. The power spectra of this extra noise suggested a 1/f(alpha) origin with best fits to the power spectrum for alpha = 0.4-0.8. This work provides the theoretical background and experimental data for understanding the bandwidth requirements and the main sources of noise in current recordings; it will be useful for minimizing noise and achieving accurate recordings.

Electrokinetics induced asymmetric transport in polymeric nanonozzles

The asymmetric geometry of polymeric nanonozzles provides two different transport directions: a converging direction (from the large opening to the small opening) and a diverging direction (from the small opening to the large opening). Asymmetric transport was observed in such nanochannels for both rigid polystyrene nanoparticles and flexible DNA molecules under a DC electric bias. Small, hard nanoparticles migrate easily in the diverging direction and tend to pack inside the nanochannel in the converging direction. In contrast, large, flexible DNA molecules transport better in the converging direction than in the diverging direction. A high electric field and a high velocity gradient along the tapered region produce different geometric constrictions and vortex-like particle motions for rigid nanoparticles, and also generate various coil-stretching dynamics for DNA molecules. Such nanonozzle arrays are useful in high flux and high sieving efficiency devices for biomolecule delivery or separation, and for loading trace amounts of drugs or genes for controlled drug and gene delivery.

Quantized current blockade and hydrodynamic correlations in biopolymer translocation through nanopores: evidence from multiscale simulations

We present a detailed description of biopolymer translocation through a nanopore in the presence of a solvent using an innovative multiscale methodology that treats the biopolymer at the microscopic scale as combined with a self-consistent mesoscopic description for the solvent fluid dynamics. We report evidence for quantized current blockade depending on the folding configuration and offer detailed information on the role of hydrodynamic correlations in speeding up the translocation process.

Conformation, length, and speed measurements of electrodynamically stretched DNA in nanochannels

A method is presented to rapidly and precisely measure the conformation, length, speed, and fluorescence intensity of single DNA molecules constrained by a nanochannel. DNA molecules were driven electrophoretically from a nanoslit into a nanochannel to confine and dynamically elongate them beyond their equilibrium length for repeated detection via laser-induced fluorescence spectroscopy. A single-molecule analysis algorithm was developed to analytically model bursts of fluorescence and determine the folding conformation of each stretched molecule. This technique achieved a molecular length resolution of 114 nm and an analysis time of around 20 ms per molecule, which enabled the sensitive investigation of several aspects of the physical behavior of DNA in a nanochannel. lambda-bacteriophage DNA was used to study the dependence of stretching on the applied device bias, the effect of conformation on speed, and the amount of DNA fragmentation in the device. A mixture of lambda-bacteriophage with the fragments of its own HindIII digest, a standard DNA ladder, was sized by length as well as by fluorescence intensity, which also allowed the characterization of DNA speed in a nanochannel as a function of length over two and a half orders of magnitude.

Actuatable membranes based on polypyrrole-coated vertically aligned carbon nanofibers

Nanoporous membranes are applicable to a variety of research fields due to their ability to selectively separate molecules with high efficiency. Of particular interest are methods for controlling membrane selectivity through externally applied stimuli and integrating such membrane structures within multiscale systems. Membranes comprised of deterministically grown, vertically aligned carbon nanofibers (VACNFs) are compatible with these needs. VACNF membranes can regulate molecular transport by physically selecting species as they pass between the fibers. Defined interfiber spacing allows for nanoscale control of membrane pore structure and resultant size selectivity. Subsequent physical or chemical modification of VACNF structures enables the tuning of physical pore size and chemical specificity allowing further control of membrane permeability. In this work, the dynamic physical modulation of membrane permeability that results when VACNFs are coated with an electrically actuatable polymer, polypyrrole, is demonstrated. Electrochemical reduction of polypyrrole on the VACNFs results in controlled swelling of the diameter of the nanofibers that in turn decreases the pore size. Dynamic control of membrane pore size enables selective transport and gating of nanoscale pores.

A new drug-sensing paradigm based on ion-current rectification in a conically shaped nanopore

Aims: To utilize the ion-current rectification phenomenon observed for conically shaped nanopores as the basis for designing sensors for drug molecules that adsorb to the walls of the nanopore. Methods: The conically shaped nanopore was prepared by the well-known track-etch method in a polyimide (Kapton) membrane. The ion current flowing through the nanopore was measured as a function of applied transmembrane potential in the presence of the analyte drug molecule, Hoechst 33258. Results: The pore walls in the Kapton membrane are hydrophobic yet have fixed carboxylate groups that give the walls a net negative charge. This fixed anionic surface charge causes the nanopore to rectify the ion current flowing through it. The analyte drug molecule, Hoechst 33258, is cationic yet also hydrophobic. When the membrane is exposed to this molecule, it adsorbs to the pore walls and neutralizes the anionic surface charge, thus lowering the extent of ion-current rectification. The change in rectification is proportional to the concentration of the drug. Conclusions: This nanopore sensor is selective for hydrophobic cations relative to anions, neutral molecules and less hydrophobic cations. Future work will explore ways of augmenting this hydrophobic effect-based selectivity so that more highly selective sensors can be obtained.

Noise in solid-state nanopores

We study ionic current fluctuations in solid-state nanopores over a wide frequency range and present a complete description of the noise characteristics. At low frequencies (f approximately < 100 Hz) we observe 1/f-type of noise. We analyze this low-frequency noise at different salt concentrations and find that the noise power remarkably scales linearly with the inverse number of charge carriers, in agreement with Hooge's relation. We find a Hooge parameter alpha = (1.1 +/- 0.1) x 10(-4). In the high-frequency regime (f approximately > 1 kHz), we can model the increase in current power spectral density with frequency through a calculation of the Johnson noise. Finally, we use these results to compute the signal-to-noise ratio for DNA translocation for different salt concentrations and nanopore diameters, yielding the parameters for optimal detection efficiency.

Nanoscopic porous sensors

There are thousands of different nanometer-scale pores in biology, many of which act as sensors for specific chemical agents. Recent work suggests that protein and solid-state nanopores have many potential uses in a wide variety of analytical applications. In this review we survey this field of research and discuss the prospects for advances that could be made in the near future.

Real-time imaging of surface evolution driven by variable-energy ion irradiation

We describe the design of a tandem instrument combining a low-energy electron microscope (LEEM) and a negative ion accelerator. This instrument provides video rate imaging of surface microtopography and the dynamics of its evolution during irradiation by energetic ions, at temperatures up to 1700 K. The negative ion beam is incident on the sample at normal incidence with impact energies selectable in the range 0-5 keV, and with current densities up to 30 muA/cm2 ( approximately 2 x 10(14)ions/cm2 s or approximately 0.2 ML/s). The LEEM operates at a base pressure in the 10(-9)Pa range. We describe the design and operating principles of the instrument and present examples of Pt(111) and Si(001) self-ion irradiation experiments.

Solid-state nanopore technologies for nanopore-based DNA analysis

Nanopore-based DNA analysis is a new single-molecule technique that involves monitoring the flow of ions through a narrow pore, and detecting changes in this flow as DNA molecules also pass through the pore. It has the potential to carry out a range of laboratory and medical DNA analyses, orders of magnitude faster than current methods. Initial experiments used a protein channel for its pre-defined, precise structure, but since then several approaches for the fabrication of solid-state pores have been developed. These aim to match the capabilities of biochannels, while also providing increased durability, control over pore geometry and compatibility with semiconductor and microfluidics fabrication techniques. This review summarizes each solid-state nanopore fabrication technique reported to date, and compares their advantages and disadvantages. Methods and applications for nanopore surface modification are also presented, followed by a discussion of approaches used to measure pore size, geometry and surface properties. The review concludes with an outlook on the future of solid-state nanopores.

Recapturing and trapping single molecules with a solid-state nanopore

The development of solid-state nanopores, inspired by their biological counterparts, shows great potential for the study of single macromolecules. Applications such as DNA sequencing and the exploration of protein folding require control of the dynamics of the molecule's interaction with the pore, but DNA capture by a solid-state nanopore is not well understood. By recapturing individual molecules soon after they pass through a nanopore, we reveal the mechanism by which double-stranded DNA enters the pore. The observed recapture rates and times agree with solutions of a drift-diffusion model. Electric forces draw DNA to the pore over micrometer-scale distances, and upon arrival at the pore, molecules begin translocation almost immediately. Repeated translocation of the same molecule improves measurement accuracy, offers a way to probe the chemical transformations and internal dynamics of macromolecules on sub-millisecond time and sub-micrometre length scales, and demonstrates the ability to trap, study and manipulate individual macromolecules in solution.

Nanopore current transduction analysis of protein binding to non-terminal and terminal DNA regions: analysis of transcription factor binding, retroviral DNA terminus dynamics, and retroviral integrase-DNA binding

BACKGROUND

Synthetic transcription factors (STFs) promise to offer a powerful new therapeutic against Cancer, AIDS, and genetic disease. Currently, 10% of drugs are of this type, including salicylate and tamoxifen. STFs that can appropriately target (and release) their transcription factor binding sites on native genomic DNA provide a means to directly influence cellular mRNA production. An effective mechanism for screening amongst transcription factor (TF) candidates would itself be highly valued, and such may be possible with nanopore cheminformatics methods.

RESULTS

It is hypothesized that binding targets on channel-captured molecules, that are well away from the channel-captured region, can be monitored insofar as their binding status, or history, is concerned. The first set of experiments we perform to explore this "transduction" hypothesis involve non-terminal dsDNA binding to protein (DNA TATA box receptor binding to TBP), where we show new experimental results and application of a new cheminformatics data analysis method. In the second series of experiments to explore the transduction hypothesis we examine terminal (blunt-ended) dsDNA binding to protein. We show experimental results before and after introduction of HIV's DNA integrase to a solution of bifunctional "Y" shaped aptamers that have an HIV consensus terminus exposed for interaction.

CONCLUSION

X-ray crystallographic studies have guided our understanding of DNA structure for almost a century. It is still difficult, however, to translate the sequence-directed curvature information obtained through these tools to actual systems found in solution. With a nanopore detector the sequence-dependent conformation kinetics of DNA, especially at the DNA terminus, can be studied in a new way while still in solution and on a single molecule basis.

The alpha-hemolysin nanopore transduction detector - single-molecule binding studies and immunological screening of antibodies and aptamers

BACKGROUND

Nanopore detection is based on observations of the ionic current threading a single, highly stable, nanometer-scale channel. The dimensions are such that small biomolecules and biopolymers (like DNA and peptides) can translocate or be captured in the channel. The identities of translocating or captured molecules can often be discerned, one from another, based on their channel blockade "signatures". There is a self-limiting aspect to a translocation-based detection mechanism: as the channel fits tighter around the translocating molecule the dynamic range of the ionic current signal is reduced. In this study, a lengthy, highly structure, high dynamic-range, molecular capture is sought as a key component of a transduction-based nanopore detection platform.

RESULTS

A specialized role, or device augmentation, involving bifunctional molecules has been explored. The bifunctional molecule has one function to enter and blockade the channel in an information-rich self-modulating manner, while the other function is for binding (usually), located on a non-channel-captured portion of the molecule. Part of the bifunctional molecule is, thus, external to the channel and is free to bind or rigidly link to a larger molecule of interest. What results is an event transduction detector: molecular events are directly transduced into discernible changes in the stationary statistics of the bifunctional molecule's channel blockade. Several results are presented of nanopore-based event-transduction detection.

CONCLUSION

It may be possible to directly track the bound versus unbound state of a huge variety of molecules using nanopore transduction detection.

Nanopore-based kinetics analysis of individual antibody-channel and antibody-antigen interactions

BACKGROUND

The UNO/RIC Nanopore Detector provides a new way to study the binding and conformational changes of individual antibodies. Many critical questions regarding antibody function are still unresolved, questions that can be approached in a new way with the nanopore detector.

RESULTS

We present evidence that different forms of channel blockade can be associated with the same antibody, we associate these different blockades with different orientations of "capture" of an antibody in the detector's nanometer-scale channel. We directly detect the presence of antibodies via reductions in channel current. Changes to blockade patterns upon addition of antigen suggest indirect detection of antibody/antigen binding. Similarly, DNA-hairpin anchored antibodies have been studied, where the DNA linkage is to the carboxy-terminus at the base of the antibody's Fc region, with significantly fewer types of (lengthy) capture blockades than was observed for free (un-bound) IgG antibody. The introduction of chaotropic agents and its effects on protein-protein interactions have also been observed.

CONCLUSION

Nanopore-based approaches may eventually provide a direct analysis of the complex conformational "negotiations" that occur upon binding between proteins.

A novel, fast, HMM-with-Duration implementation - for application with a new, pattern recognition informed, nanopore detector

Background

Hidden Markov Models (HMMs) provide an excellent means for structure identification and feature extraction on stochastic sequential data. An HMM-with-Duration (HMMwD) is an HMM that can also exactly model the hidden-label length (recurrence) distributions – while the regular HMM will impose a best-fit geometric distribution in its modeling/representation.

Results

A Novel, Fast, HMM-with-Duration (HMMwD) Implementation is presented, and experimental results are shown that demonstrate its performance on two-state synthetic data designed to model Nanopore Detector Data. The HMMwD experimental results are compared to (i) the ideal model and to (ii) the conventional HMM. Its accuracy is clearly an improvement over the standard HMM, and matches that of the ideal solution in many cases where the standard HMM does not. Computationally, the new HMMwD has all the speed advantages of the conventional (simpler) HMM implementation. In preliminary work shown here, HMM feature extraction is then used to establish the first pattern recognition-informed (PRI) sampling control of a Nanopore Detector Device (on a "live" data-stream).

Conclusion

The improved accuracy of the new HMMwD implementation, at the same order of computational cost as the standard HMM, is an important augmentation for applications in gene structure identification and channel current analysis, especially PRI sampling control, for example, where speed is essential. The PRI experiment was designed to inherit the high accuracy of the well characterized and distinctive blockades of the DNA hairpin molecules used as controls (or blockade "test-probes"). For this test set, the accuracy inherited is 99.9%.

Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore

Nanoscale pores have potential to be used as biosensors and are an established tool for analysing the structure and composition of single DNA or RNA molecules. Recently, nanopores have been used to measure the binding of enzymes to their DNA substrates. In this technique, a polynucleotide bound to an enzyme is drawn into the nanopore by an applied voltage. The force exerted on the charged backbone of the polynucleotide by the electric field is used to examine the enzyme-polynucleotide interactions. Here we show that a nanopore sensor can accurately identify DNA templates bound in the catalytic site of individual DNA polymerase molecules. Discrimination among unbound DNA, binary DNA/polymerase complexes, and ternary DNA/polymerase/deoxynucleotide triphosphate complexes was achieved in real time using finite state machine logic. This technique is applicable to numerous enzymes that bind or modify DNA or RNA including exonucleases, kinases and other polymerases.

Ionic conductance of nanopores in microscale analysis systems: where microfluidics meets nanofluidics

In this tutorial review we illustrate the origin and dependence on various system parameters of the ionic conductance that exists in discrete nanochannels as well as in nanoporous separation and preconcentration units contained as hybrid configurations, membranes, packed beds, or monoliths in microscale liquid phase analysis systems. A particular complexity arises as external electrical fields are superimposed on internal chemical and electrical potential gradients for tailoring molecular transport. It is demonstrated that the variety of geometries in which the microfluidic/nanofluidic interfaces are realized share common, fundamental features of coupled mass and charge transport, but that phenomena behind the key steps in a particular application can be significantly tuned, depending on the morphology of a material. Thus, the understanding of morphology-related transport in internal and external electrical potential gradients is critical to the performance of a device. This addresses a variety of geometries (slits, channels, filters, membranes, random or regular networks of pores, etc.) and applications, e. g., the gating, sensing, preconcentration, and separation in multifunctional miniaturized devices. Inherently coupled mass and charge transport through ion-permselective (charge-selective) microfluidic/nanofluidic interfaces is analyzed with a stepwise-added complexity and discussed with respect to the morphology of the charge-selective spatial domains. Within this scenario, the electrostatics and electrokinetics in microfluidic and nanofluidic channels, as well as the electrohydrodynamics evolving at microfluidic/nanofluidic interfaces, where microfluidics meets nanofluidics, define the platform of central phenomena.

Poisson-Nernst-Planck model of ion current rectification through a nanofluidic diode

We have investigated ion current rectification properties of a recently prepared bipolar nanofluidic diode. This device is based on a single conically shaped nanopore in a polymer film whose pore walls contain a sharp boundary between positively and negatively charged regions. A semiquantitative model that employs Poisson and Nernst-Planck equations predicts current-voltage curves as well as ionic concentrations and electric potential distributions in this system. We show that under certain conditions the rectification degree, defined as a ratio of currents recorded at the same voltage but opposite polarities, can reach values of over 1000 at a voltage range <-2 V,+2 V>. The role of thickness and position of the transition zone on the ion current rectification is discussed as well. We also show that the rectification degree scales with the applied voltage.

Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport

We study theoretically the feasibility of using transverse electronic transport within a nanopore for rapid DNA sequencing. Specifically, we examine the effects of the environment and detection probes on the distinguishability of the DNA bases. We find that the intrinsic measurement bandwidth of the electrodes helps the detection of single bases by averaging over the current distributions of each base. We also find that although the overall magnitude of the current may change dramatically with different detection conditions, the intrinsic distinguishability of the bases is not significantly affected by pore size and transverse field strength. The latter is the result of very effective stabilization of the DNA by the transverse field induced by the probes, so long as that field is much larger than the field that drives DNA through the pore. In addition, the ions and water together effectively screen the charge on the nucleotides, so that the electron states participating in the transport properties of the latter ones resemble those of the uncharged species. Finally, water in the environment has negligible direct influence on the transverse electrical current.

Progress toward ultrafast DNA sequencing using solid-state nanopores

BACKGROUND

Measurements of the ionic current flowing through nanometer-scale pores (nanopores) have been used to analyze single DNA and RNA molecules, with the ultimate goal of achieving ultrafast DNA sequencing. However, attempts at purely electronic measurements have not achieved the signal contrast required for single nucleotide differentiation. In this report we propose a novel method of optical detection of DNA sequence translocating through a nanopore.

METHODS

Each base of the target DNA sequence is 1st mapped onto a 2-unit code, 2 10-bp nucleotide sequence, by biochemical conversion into Designed DNA Polymers. These 2-unit codes are then hybridized to complementary, fluorescently labeled, and self-quenching molecular beacons. As the molecular beacons are sequentially unzipped during translocation through a <2-nm-wide nanopore, their fluorescent tags are unquenched and are detected by a custom-built dual-color total internal reflection fluorescence (TIRF) microscope. The 2-color optical signal is then correlated to the target DNA sequence.

RESULTS

A dual-color TIRFM microscope with single-molecule resolution was constructed, and controlled fabrication of 1-dimensional and 2-dimensional arrays of solid-state nanopores was performed. A nanofluidic cell assembly was constructed for TIRF-based optical detection of voltage-driven DNA translocation through a nanopore.

CONCLUSIONS

We present a novel nanopore-based DNA sequencing technique that uses an optical readout of DNA translocating unzipping through a nanopore. Our technique offers better single nucleotide differentiation in sequence readout, as well as the possibility of large-scale parallelism using nanopore arrays.

Single molecule analysis of bacterial polymerase chain reaction products in submicrometer fluidic channels

Laser induced fluorescence in submicrometer fluidic channels was used to characterize the synthesis of polymerase chain reaction (PCR) products from a model bacterial system in order to explore the advantages and limitations of on chip real time single molecule PCR analysis. Single oligonucleotide universal bacterial primers and PCR amplicons from the 16S rDNA of Thermobifida fusca (325 bp) were directly detected at all phases of the reaction with low sample consumption and without post-amplification purification or size screening. Primers were fluorescently labeled with single Alexa Fluor 488 or Alexa Fluor 594 fluorophores, resulting in double labeled, two color amplicons. PCR products were driven electrokinetically through a fused silica channel with a 250 nm by 500 nm rectangular cross section. Lasers with 488 nm and 568 nm wavelengths were focused and overlapped on the channel for fluorescence excitation. All molecules entering the channel were rapidly and uniformly analyzed. Photon burst analysis was used to detect and identify individual primers and amplicons, and fluorescence correlation and cross-correlation spectroscopy were used to account for analyte flow speed. Conventional gel and capillary electrophoresis were also used to characterize the PCR amplification, and the results of differences in detection sensitivity and analyte discrimination were examined. Limits were imposed by the purity and labeling efficiency of the PCR reagents, which must be improved in parallel with increases in detection sensitivity.

Electrostatic-gated transport in chemically modified glass nanopore electrodes

Electrostatic-gated transport in chemically modified glass nanopore electrodes with orifice radii as small as 15 nm is reported. A single conical-shaped nanopore in glass, with a approximately 1 microm radius Pt disk located at the pore base, is prepared by etching the exposed surface of a glass-sealed Pt nanodisk. The electrochemical response of the nanopore electrode corresponds to diffusion of redox-active species through the nanopore orifice to the Pt microdisk. Silanization of the exterior glass surface with Cl(Me)(2)Si(CH(2))(3)CN and the interior pore surface with EtO(Me)(2)Si(CH(2))(3)NH(2) introduces pH-dependent ion selectivity at the pore orifice, a consequence of the electrostatic interactions between the redox ions and protonated surface amines. Nanopore electrodes with very small pore orifice radii (< approximately 50 nm) display anion permselectively at pH < 4, as demonstrated by electrochemical measurement of transport through the pore orifice. Ion selective transport vanishes at pH > 6 or when the pore radius is significantly larger than the Debye screening length, consistent with the observed ion selectivity resulting from electrostatic interactions. The ability to introduce different surface functionalities to the interior and exterior surfaces of glass nanopores is demonstrated using fluorescence microscopy to monitor the localized covalent attachment of 5- (and 6)-carboxytetramethylrhodamine succinimidyl ester to interior pore surfaces previously silanized with EtO(Me)(2)Si(CH(2))(3)NH(2).

Poly(dimethylsiloxane)-based protein preconcentration using a nanogap generated by junction gap breakdown

Simple and efficient sample concentration tools are the key to the application of proteomics in a biological system. In this paper, we developed a method to realize a nanofluidic preconcentrator on a poly(dimethylsiloxane) (PDMS)-based microfluidic channel. The originality of our preconcentration device is the simple nanogap formation using the junction gap breakdown phenomenon between two PDMS microchannels, without using any photolithography and etching techniques. From the dc current measurement, we confirm that the nanogap formed between two microchannel junctions with approximately 80 nm depth. Using this device, we achieve the concentration volume of beta-phycoerythrin protein as high as 70 pL, which is 120-fold larger than that from our previous reports, with a concentration factor as high as 10(4) within 1 h. Also we show the availability of protein preconcentration under several different buffers (phosphate, acetate) at several different pH values (pH 5 to pH 9).

DNA conformation and base number simultaneously determined in a nanopore

When dsDNA polymers containing identical number of base pairs were electrophoresed through a nanopore in a voltage biased silicon nitride membrane, the measured time integral of blocked ionic current (the event-charge-deficit, ecd, Fologea, D., Gershow, M., Ledden, B., McNabb, D. S. et al.., Nano Lett. 2005, 5, 1905-1909) for each translocation event was the same regardless of whether the molecules were in a linear, circular relaxed, or supercoiled form. Conversely, when DNA polymers containing different numbers of base pairs were electrophoresed through a nanopore, the ecd depended strongly on, and predicted the value of, the molecule's number of base pairs. Measurements showed that the magnitude of the current blockages was strongly affected by a molecule's form. The current blockages exhibited characteristic differences that distinguished among single-stranded linear, double-stranded linear, circular relaxed, and supercoiled forms. Because the data that establish ecd are usually determined concomitantly with current blockade measurements, our results show that a single nanopore assay can simultaneously determine both DNA conformation and base number.

Langevin dynamics simulations of polymer translocation through nanopores

We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of an external driving force, we consider a polymer which is initially placed in the middle of the pore and study the escape time tau(e) required for the polymer to completely exit the pore on either side. The distribution of the escape times is wide and has a long tail. We find that tau(e) scales with the chain length N as tau(e) approximately N(1+2nu), where nu is the Flory exponent. For driven translocation, we concentrate on the influence of the friction coefficient xi, the driving force E, and the length of the chain N on the translocation time tau, which is defined as the time duration between the first monomer entering the pore and the last monomer leaving the pore. For strong driving forces, the distribution of translocation times is symmetric and narrow without a long tail and tau approximately E(-1). The influence of xi depends on the ratio between the driving and frictional forces. For intermediate xi, we find a crossover scaling for tau with N from tau approximately N(2nu) for relatively short chains to tau approximately N(1+nu) for longer chains. However, for higher xi, only tau approximately N(1+nu) is observed even for short chains, and there is no crossover behavior. This result can be explained by the fact that increasing xi increases the Rouse relaxation time of the chain, in which case even relatively short chains have no time to relax during translocation. Our results are in good agreement with previous simulations based on the fluctuating bond lattice model of polymers at intermediate friction values, but reveal additional features of dependency on friction.

Mechanism of DNA transport through pores

The transport of electrically charged macromolecules such as DNA through narrow pores is a fundamental process in life. When polymer molecules are forced to navigate through pores, their transport is controlled by entropic barriers that accompany their conformational changes. During the past decade, exciting results have emerged from single-molecule electrophysiology experiments. Specifically, the passage of single-stranded DNA/RNA through alpha-hemolysin pores and double-stranded DNA through solid-state nanopores has been investigated. By a combination of these results with the entropic barrier theory of polymer transport and macromolecular simulations, an understanding of the mechanism of DNA transport through pores has emerged.

Nanopore-based single-molecule DNA analysis

Nanopore-based DNA analysis is a single-molecule technique with revolutionary potential. It promises to carry out a range of analyses, orders of magnitude faster than current methods, including length measurement, specific sequence detection, single-molecule dynamics and even de novo sequencing. The concept involves using an applied voltage to drive DNA molecules through a narrow pore that separates chambers of electrolyte solution. This voltage also drives a flow of electrolyte ions through the pore, measured as an electric current. When molecules pass through the pore, they block the flow of ions and, thus, their structure and length can be determined based on the degree and duration of the resulting current reductions. In this review, I explain the nanopore-based DNA analysis concept and briefly explore its historical foundations, before discussing and summarizing all experimental results reported to date. I conclude with a summary of the obstacles that must be overcome for it to realize its promised potential.

A method for reproducibly preparing synthetic nanopores for resistive-pulse biosensors

There is increasing interest in using nanopores in synthetic membranes as resistive-pulse sensors for biomedical analytes. Analytes detected with prototype artificial-nanopore biosensors include drugs, DNA, proteins, and viruses. This field is, however, currently in its infancy. A key question that must be addressed in order for such sensors to progress from an interesting laboratory experiment to practical devices is: Can the artificial-nanopore sensing element be reproducibly prepared? We have been evaluating sensors that employ a conically shaped nanopore prepared by the track-etch method as the sensor element. We describe here a new two-step pore-etching procedure that allows for good reproducibility in nanopore fabrication. In addition, we describe a simple mathematical model that allows us to predict the characteristics of the pore produced given the experimental parameters of the two-step etch. This method and model constitute important steps toward developing practical, real-world, artificial-nanopore biosensors.