Nanobubbles in solid-state nanopores

Electron beam induced local crystallization of HfO2 nanopores for biosensing applications

We report the development of single, locally crystallized nanopores in HfO2 membranes for biosensing applications. HfO2 is chosen for its isoelectric point of 7.0, mechanical and chemical stability in solution, and for its potential as a high-k material for nanopore ionic field effect transistor applications. The HfO2 membrane is deposited on a graphene layer suspended over a 300 nm FIB hole, where graphene is used as the mechanical support. Exposure of the membrane to a focused electron beam causes crystallization in the vicinity of the nanopore during pore formation. We investigate the effects of crystallization on the electrical and surface properties of HfO2 films. Our surface analysis of HfO2 reveals improved hydrophilicity of crystallized HfO2, a notable advantage over the hydrophobicity of as-deposited HfO2. We also demonstrate detection of dsDNA translocation through HfO2 nanopores under various applied bias levels. In addition, our device architecture also presents a promising first step toward the realization of high-k HfO2 nanopore transistors.

Fine-tuning the size and minimizing the noise of solid-state nanopores

Solid-state nanopores have emerged as a versatile tool for the characterization of single biomolecules such as nucleic acids and proteins¹. However, the creation of a nanopore in a thin insulating membrane remains challenging. Fabrication methods involving specialized focused electron beam systems can produce well-defined nanopores, but yield of reliable and low-noise nanopores in commercially available membranes remains low^2,3 and size control is nontrivial^4,5. Here, the application of high electric fields to fine-tune the size of the nanopore while ensuring optimal low-noise performance is demonstrated. These short pulses of high electric field are used to produce a pristine electrical signal and allow for enlarging of nanopores with subnanometer precision upon prolonged exposure. This method is performed in situ in an aqueous environment using standard laboratory equipment, improving the yield and reproducibility of solid-state nanopore fabrication.

Threading immobilized DNA molecules through a solid-state nanopore at >100 μs per base rate

In pursuit of developing solid-state nanopore-based DNA sequencing technology, we have designed and constructed an apparatus that can place a DNA-tethered probe tip near a solid-state nanopore, control the DNA moving speed, and measure the ionic current change when a DNA molecule is captured and released from a nanopore. The probe tip's position is sensed and controlled by a tuning fork based feedback force sensor and a nanopositioning system. Using this newly constructed apparatus, a DNA strand moving rate of >100 μs/base or <1 nm/ms in silicon nitride nanopores has been accomplished. This rate is 10 times slower than by manipulating DNA-tethered beads using optical tweezers and 1000 times slower than free DNA translocation through solid-state nanopores reported previously, which provides enough temporal resolution to read each base on a tethered DNA molecule using available single-channel recording electronics on the market today. This apparatus can measure three signals simultaneously: ionic current through a nanopore, tip position, and tip vibrational amplitude during the process of a DNA molecule's capture and release by a nanopore. We show results of this apparatus for measuring λ DNA's capture and release distances and for current blockage signals of λ DNA molecules biotinylated with one end and with both ends tethered to a tip.

A patch-clamp ASIC for nanopore-based DNA analysis

In this paper, a fully integrated high-sensitivity patch-clamp system is proposed for single-molecule deoxyribonucleic acid (DNA) analysis using a nanopore sensor. This system is composed of two main blocks for amplification and compensation. The amplification block is composed of three stages: 1) a headstage, 2) a voltage-gain difference amplifier, and 3) a track-and-hold circuit, that amplify a minute ionic current variation sensed by the nanopore while the compensation block avoids the headstage saturation caused by the input parasitic capacitances during sensing. By employing design techniques novel for this application, such as an instrumentation--amplifier topology and a compensation switch, we minimize the deleterious effects of the input-offset voltage and the input parasitic capacitances while attaining hardware simplicity. This system is fabricated in a 0.35 μm 4M2P CMOS process and is demonstrated using an α-hemolysin protein nanopore for detection of individual molecules of single-stranded DNA that pass through the 1.5 nm-diameter pore. In future work, the refined system will functionalize single and multiple solid-state nanopores formed in integrated microfluidic devices for advanced DNA analysis, in scientific and diagnostic applications.

Fabrication and characterization of nanopores with insulated transverse nanoelectrodes for DNA sensing in salt solution

We report on the fabrication, simulation, and characterization of insulated nanoelectrodes aligned with nanopores in low-capacitance silicon nitride membrane chips. We are exploring these devices for the transverse sensing of DNA molecules as they are electrophoretically driven through the nanopore in a linear fashion. While we are currently working with relatively large nanopores (6-12 nm in diameter) to demonstrate the transverse detection of DNA, our ultimate goal is to reduce the size sufficiently to resolve individual nucleotide bases, thus sequencing DNA as it passes through the pore. We present simulations and experiments that study the impact of insulating these electrodes, which is important to localize the sensing region. We test whether the presence of nanoelectrodes or insulation affects the stability of the ionic current flowing through the nanopore, or the characteristics of DNA translocation. Finally, we summarize the common device failures and challenges encountered during fabrication and experiments, explore the causes of these failures, and make suggestions on how to overcome them in the future.

Measuring liquid meniscus velocity to determine size of nanopipette aperture

Nanopipette aperture sizes up to 25 nm are determined here using a method based on the Poiseuille law. Pressure is applied to the backside of a liquid plug placed in the widest end of the nanopipette, resulting in an air pressure tank with an aperture at the very tip of the nanopipette. Measuring the velocity of the liquid meniscus gives the air flow and thus the aperture size. Aperture determinations are in good agreement with SEM estimations and the proposed method is simple, relatively fast, and cheap.

Temperature sculpting in yoctoliter volumes

The ability to perturb large ensembles of molecules from equilibrium led to major advances in understanding reaction mechanisms in chemistry and biology. Here, we demonstrate the ability to control, measure, and make use of rapid temperature changes in fluid volumes that are commensurate with the size of single molecules. The method is based on attaching gold nanoparticles to a single nanometer-scale pore formed by a protein ion channel. Visible laser light incident on the nanoparticles causes a rapid and large increase of the adjacent solution temperature, which is estimated from the change in the nanopore ionic conductance. The temperature shift also affects the ability of individual molecules to enter into and interact with the nanopore. This technique could significantly improve sensor systems and force measurements based on single nanopores, thereby enabling a method for single molecule thermodynamics and kinetics.

Rapid fabrication and piezoelectric tuning of micro- and nanopores in single crystal quartz

We outline the fabrication of piezoelectric through-pores in crystalline quartz using a rapid micromachining process, and demonstrate piezoelectric deformation of the pore. The single-step fabrication technique combines ultraviolet (UV) laser irradiation with a thin layer of absorbing liquid in contact with the UV-transparent quartz chip. The effects of different liquid media are shown. We demonstrate that small exit pores, with diameters nearing the 193 nm laser wavelength and with a smooth periphery, can be achieved in 350 μm thick quartz wafers. Special crater features centring on the exit pores are also fabricated, and the depth of these craters are tuned. Moreover, by applying a voltage bias across the thickness of this piezoelectric wafer, we controllably contract and expand the pore diameter. We also provide a sample application of this device by piezoelectrically actuating alamethicin ion channels suspended over the deformable pore.

Precise control of the size and noise of solid-state nanopores using high electric fields

We present a methodology for preparing silicon nitride nanopores that provides in situ control of size with sub-nanometer precision while simultaneously reducing electrical noise by up to three orders of magnitude through the cyclic application of high electric fields in an aqueous environment. Over 90% of nanopores treated with this technique display desirable noise characteristics and readily exhibit translocation of double-stranded DNA molecules. Furthermore, previously used nanopores with degraded electrical properties can be rejuvenated and used for further single-molecule experiments.

Fast and automatic processing of multi-level events in nanopore translocation experiments

We have developed a method to analyze in detail, translocation events providing a novel and flexible tool for data analysis of nanopore experiments. Our program, called OpenNanopore, is based on the cumulative sums algorithm (CUSUM algorithm). This algorithm is an abrupt change detection algorithm that provides fitting of current blockages, allowing the user to easily identify the different levels in each event. Our method detects events using adaptive thresholds that adapt to low-frequency variations in the baseline. After event identification, our method uses the CUSUM algorithm to fit the levels inside every event and automatically extracts their time and amplitude information. This facilitates the statistical analysis of an event population with a given number of levels. The obtained information improves the interpretation of interactions between the molecule and nanopore. Since our program does not require any prior information about the analyzed molecules, novel molecule-nanopore interactions can be characterized. In addition our program is very fast and stable. With the progress in fabrication and control of the translocation speed, in the near future, our program could be useful in identification of the different bases of DNA.

Nanopore detection of single molecule RNAP-DNA transcription complex

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

Slowing down DNA translocation through a nanopore in lithium chloride

The charge of a DNA molecule is a crucial parameter in many DNA detection and manipulation schemes such as gel electrophoresis and lab-on-a-chip applications. Here, we study the partial reduction of the DNA charge due to counterion binding by means of nanopore translocation experiments and all-atom molecular dynamics (MD) simulations. Surprisingly, we find that the translocation time of a DNA molecule through a solid-state nanopore strongly increases as the counterions decrease in size from K(+) to Na(+) to Li(+), both for double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA). MD simulations elucidate the microscopic origin of this effect: Li(+) and Na(+) bind DNA stronger than K(+). These fundamental insights into the counterion binding to DNA also provide a practical method for achieving at least 10-fold enhanced resolution in nanopore applications.

Graphene nanopore devices for DNA sensing

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

Optical tweezers for mechanical control over DNA in a nanopore

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

Measuring single-wall carbon nanotubes with solid-state nanopores

Solid-state nanopores have been used widely to study biological polymers. Here, we expand the technique to analyze single-wall carbon nanotubes. By wrapping them in an amphiphilic layer, individual tubes can be translocated electrically through a nanopore, resulting in temporary interruptions in the trans-pore current reminiscent of measurements on DNA, RNA, and proteins. The technique may find use in discriminating nanotubes by size and thus electrical structure, facilitating their inclusion in electrical devices.

Ionic capillary evaporation in weakly charged nanopores

Using a variational field theory, we show that an electrolyte confined to a neutral cylindrical nanopore traversing a low dielectric membrane exhibits a first-order ionic liquid-vapor pseudo-phase-transition from an ionic-penetration "liquid" phase to an ionic-exclusion "vapor" phase, controlled by nanopore-modified ionic correlations and dielectric repulsion. For weakly charged nanopores, this pseudotransition survives and may shed light on the mechanism behind the rapid switching of nanopore conductivity observed in experiments.

Coherence Resonance in a Single-Walled Carbon Nanotube Ion Channel

Biological ion channels are able to generate coherent and oscillatory signals from intrinsically noisy and stochastic components for ultrasensitive discrimination with the use of stochastic resonance, a concept not yet demonstrated in human-made analogs. We show that a single-walled carbon nanotube demonstrates oscillations in electroosmotic current through its interior at specific ranges of electric field that are the signatures of coherence resonance. Stochastic pore blocking is observed when individual cations partition into the nanotube obstructing an otherwise stable proton current. The observed oscillations occur because of coupling between pore blocking and a proton-diffusion limitation at the pore mouth. The result illustrates how simple ionic transport can generate coherent waveforms within an inherently noisy environment and points to new types of nanoreactors, sensors, and nanofluidic channels based on this platform.

Ultrasensitive mycotoxin detection by STING sensors

Signal transduction by ion nano-gating (STING) technology is a label-free biosensor capable of identifying DNA and proteins. Based on a functionalized quartz nanopipette, the STING sensor includes specific recognition elements for analyte discrimination based on size, shape and charge density. A key feature of this technology is that it does not require any nanofabrication facility; each nanopipette can be easily, reproducibly, and inexpensively fabricated and tailored at the bench, thus reducing the cost and the turnaround time. Here, we show that STING sensors are capable of the ultrasensitive detection of HT-2 toxin with a detection limit of 100 fg/ml and compare the STING capabilities with respect to conventional sandwich assay techniques.

DNA translocation through graphene nanopores

We report on DNA translocations through nanopores created in graphene membranes. Devices consist of 1-5 nm thick graphene membranes with electron-beam sculpted nanopores from 5 to 10 nm in diameter. Due to the thin nature of the graphene membranes, we observe larger blocked currents than for traditional solid-state nanopores. However, ionic current noise levels are several orders of magnitude larger than those for silicon nitride nanopores. These fluctuations are reduced with the atomic-layer deposition of 5 nm of titanium dioxide over the device. Unlike traditional solid-state nanopore materials that are insulating, graphene is an excellent electrical conductor. Use of graphene as a membrane material opens the door to a new class of nanopore devices in which electronic sensing and control are performed directly at the pore.

Functionalized nanopipettes: toward label-free, single cell biosensors

Nanopipette technology has been proven to be a label-free biosensor capable of identifying DNA and proteins. The nanopipette can include specific recognition elements for analyte discrimination based on size, shape, and charge density. The fully electrical read-out and the ease and low-cost fabrication are unique features that give this technology an enormous potential. Unlike other biosensing platforms, nanopipettes can be precisely manipulated with submicron accuracy and used to study single cell dynamics. This review is focused on creative applications of nanopipette technology for biosensing. We highlight the potential of this technology with a particular attention to integration of this biosensor with single cell manipulation platforms.

Explicit and implicit modeling of nanobubbles in hydrophobic confinement

Water at normal conditions is a fluid thermodynamically close to the liquid-vapor phase coexistence and features a large surface tension. This combination can lead to interesting capillary phenomena on microscopic scales. Explicit water molecular dynamics (MD) computer simulations of hydrophobic solutes, for instance, give evidence of capillary evaporation on nanometer scales, i.e., the formation of nanometer-sized vapor bubbles (nanobubbles) between confining hydrophobic surfaces. This phenomenon has been exemplified for solutes with varying complexity, e.g., paraffin plates, coarse-grained homopolymers, biological and solid-state channels, and atomistically resolved proteins. It has been argued that nanobubbles strongly impact interactions in nanofluidic devices, translocation processes, and even in protein stability, function, and folding. As large-scale MD simulations are computationally expensive, the efficient multiscale modeling of nanobubbles and the prediction of their stability poses a formidable task to the'nanophysical' community. Recently, we have presented a conceptually novel and versatile implicit solvent model, namely, the variational implicit solvent model (VISM), which is based on a geometric energy functional. As reviewed here, first solvation studies of simple hydrophobic solutes using VISM coupled with the numerical level-set scheme show promising results, and, in particular, capture nanobubble formation and its subtle competition to local energetic potentials in hydrophobic confinement.

Detection of local protein structures along DNA using solid-state nanopores

Nanopores have been successfully employed as a new tool to rapidly detect single biopolymers, in particular DNA. When a molecule is driven through a nanopore by an externally applied electric field, it causes a characteristic temporary change in the trans-pore current. Here, we examine the translocation of DNA with discrete patches of the DNA-repair protein RecA attached along its length. Using the fact that RecA-coated DNA and bare DNA yield very different current-blockade signatures, we demonstrate that it is possible to map the locations of the proteins along the length of a single molecule using a solid-state nanopore. This is achieved at high speed and without any staining. We currently obtain a spatial resolution of about 8 nm, or 5 RecA proteins binding to 15 base pairs of DNA, and we discuss possible extensions to single protein resolution. The results are a crucial first step toward genomic screening, as they demonstrate the feasibility of reading off information along DNA at high resolution with a solid-state nanopore.

Translocation of RecA-coated double-stranded DNA through solid-state nanopores

We report translocation of double-stranded DNA (dsDNA) molecules that are coated with RecA protein through solid-state nanopores. Translocation measurements show current-blockade events with a wide variety in time duration (10-4-10-1 s) and conductance blockade values (3-14 nS). Large blockades (11.4+/-0.7 nS) are identified as being caused by translocations of RecA-dsDNA filaments. We confirm these results through a variety of methods, including changing molecular length and using an optical tweezer system to deliver bead-functionalized molecules to the nanopore. We further distinguish two different regimes of translocation: a low-voltage regime (<150 mV) in which the event rate increases exponentially with voltage, and a high-voltage regime in which it remains constant. Our results open possibilities for a variety of future experiments with (partly) protein-coated DNA molecules, which is interesting for both fundamental science and genomic screening applications.

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

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

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

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

Low-frequency noise in solid-state nanopores

Low-frequency ionic current noise in solid-state nanopores imposes a limitation on the time resolution achieved in translocation experiments. Recently, this 1/f noise was described as obeying Hooge's phenomenological relation, where the noise scales inversely with the number of charge carriers present. Here, we consider an alternative model in which the low-frequency noise originates from surface charge fluctuations. We compare the models and show that Hooge's relation gives the best description for the low-frequency noise in solid-state nanopores over the entire salt regime from 10(-3) to 1.6 M KCl.

Inserting and manipulating DNA in a nanopore with optical tweezers

The translocation of small molecules and polymers is an integral process for the functioning of living cells. Many of the basic physical, chemical, and biological interactions have not yet been studied because they are not directly experimentally accessible. We have shown that a combination of optical tweezers, single solid-state nanopores, and electrophysiological ionic current detection enable deeper insight into the behavior of polymers in confinement. Here we describe the experimental procedures that are necessary to manipulate single biopolymers in a single nanopore, not only by electrical fields, but also through mechanical forces using optical tweezers.

OPTIMIZING COLLAGEN TRANSPORT THROUGH TRACK-ETCHED NANOPORES

Polymer transport through nanopores is a potentially powerful tool for separation and organization of molecules in biotechnology applications. Our goal is to produce aligned collagen fibrils by mimicking cell-mediated collagen assembly: driving collagen monomers in solution through the aligned nanopores in track-etched membranes followed by fibrillogenesis at the pore exit. We examined type I atelo-collagen monomer transport in neutral, cold solution through polycarbonate track-etched membranes comprising 80-nm-diameter, 6-μm-long pores at 2% areal fraction. Source concentrations of 1.0, 2.8 and 7.0 mg/ml and pressure differentials of 0, 10 and 20 inH(2)O were used. Membrane surfaces were hydrophilized via covalent poly(ethylene-glycol) binding to limit solute-membrane interaction. Collagen transport through the nanopores was a non-intuitive process due to the complex behavior of this associating molecule in semi-dilute solution. Nonetheless, a modified open pore model provided reasonable predictions of transport parameters. Transport rates were concentration- and pressure-dependent, with diffusivities across the membrane in semi-dilute solution two-fold those in dilute solution, possibly via cooperative diffusion or polymer entrainment. The most significant enhancement of collagen transport was accomplished by membrane hydrophilization. The highest concentration transported (5.99±2.58 mg/ml) with the highest monomer flux (2.60±0.49 ×10(3) molecules s(-1) pore(-1)) was observed using 2.8 mg collagen/ml, 10 inH(2)O and hydrophilic membranes.

Pyridine ligand rotation in self-assembled trigonal prisms. Evidence for intracage solvent vapor bubbles

The rate of interconversion of the two inequivalent edges of the pyridine rings in the trigonal prism 3c, self-assembled from 3 equiv of the star connector, tetrakis[4-(4-pyridylethynyl)phenyl]cyclobutadienecyclopentadienylcobalt, and 6 equiv of a platinum linker, cis-(Me3P)2Pt(2+) 2 TfO(-), was determined by DNMR in nitromethane. It exhibits a highly unusual bilinear Eyring plot. In the low temperature regime, the activation enthalpy DeltaH(double dagger) is approximately 12 kcal/mol and an activation entropy DeltaS(double dagger) ranges from approximately -15 to approximately 0 cal/mol x K as a function of the nature and concentration of the anions present. The reaction is attributed to hindered rotation of the pyridine rings about the Pt-N bond, facilitated by a tight pairing with a counterion. Above a counterion-dependent limiting temperature, DeltaH(double dagger) and DeltaS(double dagger) change abruptly to approximately 35 kcal/mol and approximately 60 cal/mol x K, respectively. The changes largely compensate, such that the reactions have comparable rates in the two regimes, both amenable to DNMR measurement, but their mechanisms clearly differ. Several kinetic models for the involvement of ion pairing equilibria fit the observed data nearly equally well, and they all contain a reaction step with high DeltaH(double dagger) and DeltaS(double dagger) values in the high-temperature regime. Its mechanism is proposed to involve a counterion-assisted reversible dissociation of one or two adjacent Pt-N bonds, followed by nearly free rotation of the terminal pyridine ring or rings and subsequent bond reclosure, which is similar to the last presumed step in the initial prism assembly. An interpretation of the very high DeltaS(double dagger) value is suggested by molecular dynamics calculations: at equilibrium, there is a bubble of gaseous nitromethane solvent inside the prism, and it collapses when the prism opens as the transition state is reached. A simple calculation of the entropy of cavitation provides quantitative support for this tentative proposal. The presence of such voids might be generally important for the formation and properties of self-assembled cages.

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.

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.

Design of a solid-state nanopore-based platform for single-molecule spectroscopy

We numerically assess the light propagation and distribution characteristics of electromagnetic fields on nanopores formed in dielectric and metal/dielectric membranes using a frequency-domain finite element method (3D full-wave electromagnetic field simulation). Results of such studies were used to identify aluminum as an ideal material for use in optically thick metal/dielectric membranes. The comparison between SiN and Al/SiN membranes (with and without a submicron sized aperture) was numerically and experimentally shown to verify the effect of optically thick metal layers on light propagation and fluorescence excitation. The cut-off behavior for Al/SiN membranes with varying pore diameters was investigated in terms of light propagation, distribution of electromagnetic fields, and light attenuation characteristics.

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.

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.

Controlling DNA capture and propagation through artificial nanopores

Electrophorescing biopolymers across nanopores modulates the ionic current through the pore, revealing the polymer's diameter, length, and conformation. The rapidity of polymer translocation ( approximately 30,000 bp/ms) in this geometry greatly limits the information that can be obtained for each base. Here we show that the translocation speed of lambda-DNA through artificial nanopores can be reduced using optical tweezers. DNAs coupled to optically trapped beads were presented to nanopores. DNAs initially placed up to several micrometers from the pore could be captured. Subsequently, the optical tweezers reduced translocation speeds to 150 bp/ms, about 200-fold slower than free DNA. Moreover, the optical tweezers allowed us to "floss" single polymers back and forth through the pore. The combination of controlled sample presentation, greatly slowed translocation speeds, and repeated electrophoresis of single DNAs removes several barriers to using artificial nanopores for sequencing, haplotyping, and characterization of protein-DNA interactions.

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.

A nanoscale gas state

We show that a very thin (5-80 nm) gas phase can exist for a long time (>1 h) at the interface between a hydrophobic solid and water. We create the gas phase from CO2, which allows us to determine the chemical identity, phase state, and density via infrared spectroscopy. The average density reveals that the gas is at approximately atmospheric pressure, which explains the unexpectedly long lifetime of the gas phase under ambient conditions. The nanoscale gas phase is reproducibly created under conditions where gas solubility is varied.