Ion-beam sculpting at nanometre length scales

Rapid and precise scanning helium ion microscope milling of solid-state nanopores for biomolecule detection

We report the formation of solid-state nanopores using a scanning helium ion microscope. The fabrication process offers the advantage of high sample throughput along with fine control over nanopore dimensions, producing single pores with diameters below 4 nm. Electronic noise associated with ion transport through the resultant pores is found to be comparable with levels measured on devices made with the established technique of transmission electron microscope milling. We demonstrate the utility of our nanopores for biomolecular analysis by measuring the passage of double-strand DNA.

Theoretical and experimental study of nanopore drilling by a focused electron beam in transmission electron microscopy

Sub-10 nm nanopores drilled by a focused electron beam in a transmission electron microscope are widely used in solid-state nanopore devices for DNA translocation. However, there still remains much controversy surrounding the drilling mechanism. In order to explain the drilling of nanopores by electrons, we undertook a theoretical consideration of the energy transfer from the fast electrons to the solid through such mechanisms as elastic and inelastic scattering. According to the calculations based on the scattering cross-section, the direct atomic displacement cross-section induced by elastic scattering increases with increasing incident electron energy, while the ionization cross-section and temperature increment decrease. We performed nanopore drilling in a Si3N4 membrane using two different electron energies, 200 and 300 kV, to identify the drilling mechanism. The dependence of the nanopore drilling on the incident electron energy was well matched with the direct atomic displacement.

Large area flexible SERS active substrates using engineered nanostructures

Surface enhanced Raman scattering (SERS) is an analytical sensing method that provides label-free detection, molecularly specific information, and extremely high sensitivity. The Raman enhancement that makes this method attractive is mainly attributed to the local amplification of the incident electromagnetic field that occurs when a surface plasmon mode is excited at a metallic nanostructure. Here, we present a simple, cost effective method for creating flexible, large area SERS-active substrates using a new technique we call shadow mask assisted evaporation (SMAE). The advantage of large, flexible SERS substrates such as these is they have more area for multiplexing and can be incorporated into irregular surfaces such as clothing. We demonstrate the formation of four different types of nanostructure arrays (pillar, nib, ellipsoidal cylinder, and triangular tip) by controlling the evaporation angle, substrate rotation, and deposition rate of metals onto anodized alumina nanoporous membranes as large as 27 mm. In addition, we present experimental results showing how a hybrid structure comprising of gold nanospheres embedded in a silver nano-pillar structure can be used to obtain a 50× SERS enhancement over the raw nanoparticles themselves.

Controlling molecular transport through nanopores

Nanopores are emerging as powerful tools for the detection and identification of macromolecules in aqueous solution. In this review, we discuss the recent development of active and passive controls over molecular transport through nanopores with emphasis on biosensing applications. We give an overview of the solutions developed to enhance the sensitivity and specificity of the resistive-pulse technique based on biological and solid-state nanopores.

Ion-erosion induced surface nanoporosity and nanotopography on Si

The low-energy ion-bombardment induced surface nanotopography and the nanopatterning of Si has been simulated by atomistic simulations using an approach based on molecular dynamics (MD). In order to speed up simulations a reasonable cutoff in simulation time and increased cooling rates for keeping in hand the system temperature have been used. We get an unexpectedly rich variety of disordered nanopatterns formed by the self-organization of the crater rims and adatoms islands generated by the individual ion impacts. Our results reveal that the low-energy (0.5 keV impact energy) ion-sputtered Si surface is not smooth at the sub-20 nm length scale and deep nanoholes rule the landscape. Moreover substantial nanoporosity is found beneath the surface with the size range of a few nanometer. Scanning tunneling microscopy (STM) images are also shown obtained for low-fluence ion-sputtering of Si at 2 keV impact energy at 30° angle of incidence. STM images reveal similar features obtained by computer simulations: nanoholes can be seen with a few nanometer diameter. The overall topography landscape as well as the rms surface roughness also show similar features for the images obtained by STM or MD at 2 keV impact energy. The applied approach could make it possible the simulation of nanotopographic images at the molecular dynamics level of theory and could help resolve scanning probe microscopy images in the sub-20 nm length scale regime.

Unzipping of Double-stranded DNA in Engineered α-Hemolysin Pores

Biological protein α-hemolysin nanopore is under intense investigation as a potential platform for rapid and low-cost DNA sequencing. However, due to its narrow constriction, analysis of DNA in the α-hemolysin pore has long time been restricted to single strands. In this paper, we report that by introducing new surface functional groups into the α-hemolysin pore, facilitated unzipping of double-stranded DNA through the channel could be achieved. Since the mean residence time of the DNA events is dependent on the length of the duplex, and also varies with the nucleotide base composition, the modified protein pore approach offers the potential for rapid double-stranded DNA analysis, including sequencing.

Dynamics of completely unfolded and native proteins through solid-state nanopores as a function of electric driving force

We report experimentally the dynamic properties of the entry and transport of unfolded and native proteins through a solid-state nanopore as a function of applied voltage, and we discuss the experimental data obtained as compared to theory. We show an exponential increase in the event frequency of current blockades and an exponential decrease in transport times as a function of the electric driving force. The normalized current blockage ratio remains constant or decreases for folded or unfolded proteins, respectively, as a function of the transmembrane potential. The unfolded protein is stretched under the electric driving force. The dwell time of native compact proteins in the pore is almost 1 order of magnitude longer than that of unfolded proteins, and the event frequency for both protein conformations is low. We discuss the possible phenomena hindering the transport of proteins through the pores, which could explain these anomalous dynamics, in particular, electro-osmotic counterflow and protein adsorption on the nanopore wall.

Coarse-grained molecular dynamics simulation of DNA translocation in chemically modified nanopores

Solid-state nanopores provide a direct means to detect and analyze DNA and proteins. In a typical setup, the DNA molecules travel through a nanopore under electrophoretic voltage bias. The nanopore is sandwiched between two chambers that are filled with ionic solution. A major challenge in using solid-state nanopores for DNA sequencing and gene detection is to improve their selectivity and detection sensitivity. To achieve these goals, one solution is to functionalize the nanopores by chemically modifying the pore walls with silanes or nucleic acids. However, little is known about molecular interactions in functionalized nanopores. This paper presents DNA translocation dynamics and the mechanism of DNA sequencing in a functionalized nanopore through a coarse-grained molecular dynamics model. The DNA nucleotide is coarse-grained into two interaction sites: one site corresponds to the base group and the other encompasses the phosphate and sugar groups. The water molecules are included in the model implicitly through Langevin dynamics. The coarse-grained model immensely improves the computational efficiency while still capturing the essential translocation dynamics. The model characterizes important physical properties of functionalized nanopores such as the effective pore diameter and effect of biasing voltage on the DNA translocation dynamics. The model reveals a nonlinear relationship between translocation speed of DNA and applied voltage. Moreover, DNA translocation in nanopores functionalized with hairpin-loop (HPL) DNA and single-stranded DNA (ss-DNA) shows significant differences: a target DNA is found to translocate through a ss-DNA coated nanopore 9 times faster than through an HPL coated one at a bias of 100 mV, putatively from lower stiffness of ss-DNA than that for HPL. The DNA translocation speed is also largely influenced by interaction potential between the DNA and surface-tethered molecules. The results reveal that such selective translocation, distinctly different translocation dynamics of target DNA molecules largely stem from the flexibility and orientation of the surface-tethered molecules. These findings can significantly impact the rational design of DNA transport experiments leading to rapid molecule-level diagnostics.

Shrinking of Solid-state Nanopores by Direct Thermal Heating

Solid-state nanopores have emerged as useful single-molecule sensors for DNA and proteins. A novel and simple technique for solid-state nanopore fabrication is reported here. The process involves direct thermal heating of 100 to 300 nm nanopores, made by focused ion beam (FIB) milling in free-standing membranes. Direct heating results in shrinking of the silicon dioxide nanopores. The free-standing silicon dioxide membrane is softened and adatoms diffuse to a lower surface free energy. The model predicts the dynamics of the shrinking process as validated by experiments. The method described herein, can process many samples at one time. The inbuilt stress in the oxide film is also reduced due to annealing. The surface composition of the pore walls remains the same during the shrinking process. The linear shrinkage rate gives a reproducible way to control the diameter of a pore with nanometer precision.

A novel method of fabricating a nanopore based on a glass tube for single-molecule detection

A novel nanopore fabrication method is reported by thermally pulling a glass tube in a two step process. The principle is based on the physical footprint of the phase change of the paraffin sealed inside the glass tube to form a nanocavity in the broken terminal during the second step of the pulling process. A nanopore with minimum diameter of 40 nm is fabricated after rubbing the terminal to make the channel through it. IgG molecules are used to test whether the nanopore can discriminate biomolecules. A transient current change from increasing to decreasing was observed when IgG molecules passed through the nanopore in pure water, suggesting that the IgG has a Y-shaped structure. This is in agreement with the known IgG structure. Experiments also uncovered that the train pulse signals due to the translocation of the biomolecules are sensitive to salt solutions. It was found that the negative amplitude of the pulse signal can be screened while the IgG molecules are mixed with a low KCL concentration solution. When changing from low to high salt concentrations we observed an inversion of the peak orientation. This is attributed to the competing conductance contribution to the ionic currents from the charges carried by the IgG molecules themselves and the exclusive ions blocked by the IgG molecules, suggesting that the salt ions in the solution may hide the true biomolecule structure.

Controlling protein translocation through nanopores with bio-inspired fluid walls

Synthetic nanopores have been used to study individual biomolecules in high throughput, but their performance as sensors does not match that of biological ion channels. Challenges include control of nanopore diameters and surface chemistry, modification of the translocation times of single-molecule analytes through nanopores, and prevention of non-specific interactions with pore walls. Here, inspired by the olfactory sensilla of insect antennae, we show that coating nanopores with a fluid lipid bilayer tailors their surface chemistry and allows fine-tuning and dynamic variation of pore diameters in subnanometre increments. Incorporation of mobile ligands in the lipid bilayer conferred specificity and slowed the translocation of targeted proteins sufficiently to time-resolve translocation events of individual proteins. Lipid coatings also prevented pores from clogging, eliminated non-specific binding and enabled the translocation of amyloid-beta (Aβ) oligomers and fibrils. Through combined analysis of their translocation time, volume, charge, shape and ligand affinity, different proteins were identified.

Thermal activation and saturation of ion beam sculpting

We report a material-dependent critical temperature for ion beam sculpting of nanopores in amorphous materials under keV ion irradiation. At temperatures below the critical temperature, irradiated pores open at a rate that soon saturates with decreasing temperature. At temperatures above the critical temperature, the pore closing rate rises rapidly and eventually saturates with increasing temperature. The observed behavior is well described by a model based on adatom diffusion, but is difficult to reconcile with an ion-stimulated viscous flow model.

Controlled deformation of Si3N4 nanopores using focused electron beam in a transmission electron microscope

The controllable deformation of nanopores was realized by moving a convergent electron beam in a high-resolution transmission electron microscope. Nanostructures with the desired geometries were successfully fabricated from the original nanopores in 100 nm-thick and 260 nm-thick Si(3)N(4) membranes. The formation dynamics is a competition process between the knock-on effect of the high-energy electron beam and surface tension driven shrinkage. This approach can be used to finely tune critical dimensions and deform nanopores to particular desired geometries with single-nanometer precision, which offers substantial opportunities in flexibly fabricating nanostructures for various applications such as nanoelectronics and nanofluidics.

Direct Focused Ion Beam Drilling of Nanopores

Focused 30keV gallium ion beam, single-pixel drilling combined with backside particle detection is used to fabricate pores having exit diameters as small as ~11 nm in 200 nm-thick silicon nitride membranes. The backside channelplate detector response obtained about the onset of breakthrough is interpreted by plan-view transmission electron microscopy investigations of hole morphology. Immediately prior to breakthrough, there is a rise in detector signal as the local membrane thickness is reduced. This likely occurs as a result of ion transmission and, possibly, forward sputtering. At the dose required for breakthrough a maximum detector signal is obtained thus providing a potential method for end point detection. The focused ion drilling technique avoids broad area beam exposure methods that are often used to reduce hole diameter to nanometer dimension. In addition, the current approach overcomes difficulties in determining a required dose for breakthrough such as those that arise from an inhomogeneous membrane thickness, redeposition, or ion channeling.

Rectification of the current in alpha-hemolysin pore depends on the cation type: the alkali series probed by MD simulations and experiments

A striking feature of the alpha-hemolysin channel-a prime candidate for biotechnological applications-is the dependence of its ionic conductance on the magnitude and direction of the applied bias. Through a combination of lipid bilayer single-channel recording and molecular dynamics (MD) simulations, we characterized the current-voltage relationship of alpha-hemolysin for all alkali chloride salts at neutral pH. The rectification of the ionic current was found to depend on the type of cations and increase from Li(+) to Cs(+). Analysis of the MD trajectories yielded a simple quantitative model that related the ionic current to the electrostatic potential, the concentration and effective mobility of ions in the channel. MD simulations reveal that the major contribution to the current asymmetry and rectification properties originates from the cationic contribution to the current that is significantly reduced in a cationic dependent way when the membrane polarity is reversed. The variation of chloride current was found to be less important. We report that the differential affinity of cations for the charged residues positioned at the channel's end modulates the number of ions inside the channel stem thus affecting the current properties. Through direct comparison of simulation and experiment, this study evaluates the accuracy of the MD method for prediction of the asymmetric, voltage dependent conductances of a membrane channel.

Study on the Size Shrinking and Shape Changing of Solid-State Nanopores

Nanopores etched in the solid-state membranes have become the hotpot of nanotechnology research. Various methods for fabricating solid-state nanopores have been developed and reported, but the fabrication of nanopore is also a difficult challenge. In this paper, we milled nanopores of different sizes in the free-stand and low-stress solid-state membranes. And then the area around nanopores were scanned with the diffused ion beam, we found that the sediment around will melt and the shape of the nanopore becomes circular.

Genome sequencing and assembly

Decoding the genome sequence is becoming a fundamental tool for molecular, genetic, and genomic studies. This chapter reviews the history of DNA sequencing and technical principles of different sequencing platforms, and compares the strengths and weaknesses of different techniques for high-throughput genome sequencing applications are compared. It also covers brief descriptions on genome assembly and its validation.

Sequence dependence of the binding energy in chaperone-driven polymer translocation through a nanopore

We study the translocation of stiff polymers through a nanopore, driven by the chemical-potential gradient exerted by binding proteins (chaperones) on the trans side of the pore. Bound chaperones prevent backsliding through the pore and, therefore, partially rectify the polymer passage. We show that the sequence of chain monomers with different binding affinity for the chaperones significantly affects the translocation dynamics. In particular, we investigate the effect of the nearest-neighbor adjacency probability of the two monomer types. Depending on the magnitude of the involved binding energies, the translocation speed may either increase or decrease with the adjacency probability. We determine the mean first passage time and show that, by tuning the effective binding energy, the motion changes continuously from purely diffusive to ballistic translocation.

Transport and sensing in nanofluidic devices

Ion transport and sensing in nanofluidic devices are receiving a great deal of attention because of their unique transport properties and potential analytical applications. Some aspects of microscale transport transfer directly to the nanoscale, but nanofluidic systems can be significantly influenced by phenomena such as double-layer overlap, surface charge, ion-current rectification, diffusion, and entropic forces, which are either insignificant or absent in larger microchannels. Micro- and nanofabrication techniques create features with a wide range of well-defined geometries and dimensions in synthetic and solid-state substrates. Moreover, these techniques permit coupling of multiple nano- and microscale elements, which can execute various functions. We discuss basic nanofluidic architectures, material transport properties through single and multiple nanochannels, and characterization of single particles by resistive-pulse sensing.

Pink noise of ionic conductance through single artificial nanopores revisited

We report voltage-clamp measurements through single conical nanopore obtained by chemical etching of a single ion track in polyimide film. Special attention is paid to the pink noise of the ionic current (i.e., 1/f noise) measured with different filling liquids. The relative pink-noise amplitude is almost independent of concentration and pH for KCl solutions, but varies strongly using ionic liquids. In particular, we show that depending on the ionic liquid, the transport of charge carriers is strongly facilitated (low noise and higher conductivity than in the bulk) or jammed. These results show that the origin of the pink noise can be ascribed neither to fluctuations of the pore geometry nor to the pore wall charges, but rather to a cooperative effect on ions motion in confined geometry.

Multiplexed parallel single transport recordings on nanopore arrays

We introduce a nanofabricated silicon chip for massively multiplexed analysis of membrane channels and transporters in suspended lipid membranes that does not require any surface modification or organic solvent. Transport processes through single membrane complexes are monitored by fluorescence. The chip consists of an array of well-defined nanopores, addressing an individual pyramidal back-reflecting 30-fL compartment. The setup allows simultaneous analyses of ∼1,000 single transmembrane events in one field of view, observing translocation kinetics of transmembrane complexes.

Shape-controlled nanopores in single crystals

Nanometer length-scale holes (nanopores) are often formed in amorphous materials for fundamental studies of molecular mass transport. In the current study, electron beam irradiation in the transmission electron microscope was used to form nanopores in a crystalline material (Si). Analysis of the nanopores showed that they are formed by knock-on of atoms by the high energy incident electron beam, and surface diffusion is partially responsible for the hour-glass shapes that are found for some nanopores. Energetically favorable three-dimensional shapes of nanopores were simulated, and the nanopores simulated in the model crystalline material were found to be more stable than the nanopores simulated in the amorphous material. The nanopore shape was also found to depend on the nanopore diameter-to-length ratio. Based on the above, we demonstrate the advantage in using a crystalline material for nanopore formation and show that control of the three-dimensional shape of nanopores formed by electron beam irradiation is possible.

A robust nanofluidic membrane with tunable zero-order release for implantable dose specific drug delivery

This manuscript demonstrates a mechanically robust implantable nanofluidic membrane capable of tunable long-term zero-order release of therapeutic agents in ranges relevant for clinical applications. The membrane, with nanochannels as small as 5 nm, allows for the independent control of both dosage and mechanical strength through the integration of high-density short nanochannels parallel to the membrane surface with perpendicular micro- and macrochannels for interfacing with the ambient solutions. These nanofluidic membranes are created using precision silicon fabrication techniques on silicon-on-insulator substrates enabling exquisite control over the monodispersed nanochannel dimensions and surface roughness. Zero-order release of analytes is achieved by exploiting molecule to surface interactions which dominate diffusive transport when fluids are confined to the nanoscale. In this study we investigate the nanofluidic membrane performance using custom diffusion and gas testing apparatuses to quantify molecular release rate and process uniformity as well as mechanical strength using a gas based burst test. The kinetics of the constrained zero-order release is probed with molecules presenting a range of sizes, charge states, and structural conformations. Finally, an optimal ratio of the molecular hydrodynamic diameter to the nanochannel dimension is determined to assure zero-order release for each tested molecule.

Fabrication and electrical characterization of a pore-cavity-pore device

We present a solid state nanopore device structure comprising two nanopores which are stacked above each other and connected via a pyramidal cavity of 10 fl volume. The process of fabrication of the pore-cavity-pore device (PCP) relies on the formation of one pore in a Si(3)N(4) membrane by electron beam lithography, while the other pore is chemically etched into the Si carrier by a feedback controlled process. The dimensions of the two nanopores as well as the cavity can be adjusted independently, which is confirmed by transmission electron microscopy. The PCP device is characterized with respect to its electrical properties, including noise analysis and impedance spectroscopy. An equivalent circuit model is identified and resistance, capacitance, and dielectric loss factors are obtained. Potential and electric field distributions inside the electrically biased device are simulated by finite element methods. The low noise characteristics of the PCP device (comparable to a single solid state nanopore) make it suitable for the stochastic sensing of single molecules; moreover, the pore-cavity-pore architecture allows for novel kinds of experiments including the trapping of single nano-objects and single molecule time-of-flight measurements.

Translocation events in a single walled carbon nanotube

Translocation of DNA oligomers through a single walled carbon nanotube was demonstrated recently. Translocation events are accompanied by giant current pulses, the origin of which remains obscure. Here, we show that introduction of a nucleotide alone, guanosine triphosphate into the input reservoir of a carbon nanotube nanofluidic also gives giant current pulses. Taken together with data on oligomer translocation, theses new results suggest that pulse width has a non-linear, power-law dependence on the number of nucleotides in a DNA molecule. We have also measured the time for the onset of DNA translocation pulses after bias reversal, finding that the time for the onset of translocation is directly proportional to the period of bias reversal.

Evidence that small proteins translocate through silicon nitride pores in a folded conformation

The interaction of three proteins (histidine-containing phosphocarrier protein, HPr, calmodulin, CaM, and maltose binding protein, MBP) with synthetic silicon nitride (SiN(x)) membranes has been studied. The proteins which have a net negative charge were electrophoretically driven into pores of 7 and 5 nm diameter with a nominal length of 15 nm. The % blockade current and event duration were measured at three different voltages. For a translocation event it was expected that the % block would be constant with voltage whilst the event duration would decrease with increasing voltage. On the basis of these criteria, we deduce that MBP whose largest dimension is 6.5 nm does not translocate whereas up to 40% of CaM molecules can translocate the 7 nm pore as can a majority of HPr molecules, with some translocations being observed for the 5 nm pore. For translocation events the magnitude of the % blockade current is consistent with a folded conformation of the proteins surrounded by a hydration shell of 0.5-1.0 nm.

Dehydration and ionic conductance quantization in nanopores

There has been tremendous experimental progress in the last decade in identifying the structure and function of biological pores (ion channels) and fabricating synthetic pores. Despite this progress, many questions still remain about the mechanisms and universal features of ionic transport in these systems. In this paper, we examine the use of nanopores to probe ion transport and to construct functional nanoscale devices. Specifically, we focus on the newly predicted phenomenon of quantized ionic conductance in nanopores as a function of the effective pore radius--a prediction that yields a particularly transparent way to probe the contribution of dehydration to ionic transport. We study the role of ionic species in the formation of hydration layers inside and outside of pores. We find that the ion type plays only a minor role in the radial positions of the predicted steps in the ion conductance. However, ions with higher valency form stronger hydration shells, and thus, provide even more pronounced, and therefore, more easily detected, drops in the ionic current. Measuring this phenomenon directly, or from the resulting noise, with synthetic nanopores would provide evidence of the deviation from macroscopic (continuum) dielectric behavior due to microscopic features at the nanoscale and may shed light on the behavior of ions in more complex biological channels.

Precise electrochemical fabrication of sub-20 nm solid-state nanopores for single-molecule biosensing

It has recently been shown that solid-state nanometer-scale pores ('nanopores') can be used as highly sensitive single-molecule sensors. For example, electrophoretic translocation of DNA, RNA and proteins through such nanopores has enabled both detection and structural analysis of these complex biomolecules. Control over the nanopore size is critical as the pore must be comparable in size to the analyte molecule in question. The most widely used fabrication methods are based on focused electron or ion beams and thus require (scanning) transmission electron microscopy and focused ion beam (FIB) instrumentation. Even though very small pores have been made using these approaches, several issues remain. These include the requirement of being restricted to rather thin, mechanically less stable membranes, particularly for pore diameters in the single-digit nanometer range, lack of control of the surface properties at and inside the nanopore, and finally, the fabrication cost. In the proof-of-concept study, we report on a novel and simple route for fabricating metal nanopores with apparent diameters below 20 nm using electrodeposition and real-time ionic current feedback in solution. This fabrication approach inserts considerable flexibility into the kinds of platforms that can be used and the nanopore membrane material. Starting from much larger pores, which are straightforward to make using FIB or other semiconductor fabrication methods, we electrodeposit Pt at the nanopore interface while monitoring its ionic conductance at the same time in a bi-potentiostatic setup. Due to the deposition of Pt, the nanopore decreases in size, resulting in a decrease of the pore conductance. Once a desired pore conductance has been reached, the electrodeposition process is stopped by switching the potential of the membrane electrode and the fabrication process is complete. Furthermore, we demonstrate that these pores can be used for single-biomolecule analysis, such as that of λ-DNA, which we use in a proof-of-concept study. Importantly, our approach is applicable to single nanopores as well as nanopore arrays, and can easily be extended to deposits of metal other than Pt.

Chemically modified solid state nanopores for high throughput nanoparticle separation

The separation of biomolecules and other nanoparticles is a vital step in several analytical and diagnostic techniques. Towards this end we present a solid state nanopore-based set-up as an efficient separation platform. The translocation of charged particles through a nanopore was first modeled mathematically using the multi-ion model and the surface charge density of the nanopore membrane was identified as a critical parameter that determines the selectivity of the membrane and the throughput of the separation process. Drawing from these simulations a single 150 nm pore was fabricated in a 50 nm thick free-standing silicon nitride membrane by focused-ion-beam milling and was chemically modified with (3-aminopropyl)triethoxysilane to change its surface charge density. This chemically modified membrane was then used to separate 22 and 58 nm polystyrene nanoparticles in solution. Once optimized, this approach can readily be scaled up to nanopore arrays which would function as a key component of next-generation nanosieving systems.

Detection of urea-induced internal denaturation of dsDNA using solid-state nanopores

The ability to detect and measure dsDNA thermal fluctuations is of immense importance in understanding the underlying mechanisms responsible for transcription and replication regulation. We describe here the ability of solid-state nanopores to detect sub-nanometer changes in DNA structure as a result of chemically enhanced thermal fluctuations. In this study, we investigate the subtle changes in the mean effective diameter of a dsDNA molecule with 3-5 nm solid-state nanopores as a function of urea concentration and the DNA's AT content. Our studies reveal an increase in the mean effective diameter of a DNA molecule of approximately 0.6 nm at 8.7 M urea. In agreement with the mechanism of DNA local denaturation, we observe a sigmoid dependence of these effects on urea concentration. We find that the translocation times in urea are markedly slower than would be expected if the dynamics were governed primarily by viscous effects. Furthermore, we find that the sensitivity of the nanopore is sufficient to statistically differentiate between DNA molecules of nearly identical lengths differing only in sequence and AT content when placed in 3.5 M urea. Our results demonstrate that nanopores can detect subtle structural changes and are thus a valuable tool for detecting differences in biomolecules' environment.

Current oscillations generated by precipitate formation in the mixing zone between two solutions inside a nanopore

Unlike biological protein pores in lipid membranes, nanopores fabricated in synthetic materials can withstand a wide range of environmental conditions including the presence of organic solvents. This capability expands the potential of synthetic nanopores to monitor chemical reactions occurring at the interface between solutions of organic and aqueous character. In this work, nanopores fabricated in borosilicate glass or silicon nitride connected a predominantly organic solvent to an aqueous solvent, thereby generating a mixing zone between these solutions inside the pore. This configuration was exploited to precipitate small organic molecules with low aqueous solubility inside the nanopores, and concomitantly, to monitor this precipitation by the decrease of the ionic conductance through the nanopores over time. Hence, this method provides a means to induce and investigate the formation of nanoprecipitates or nanoparticles. Interestingly, precipitates with a slight electric charge were cleared from the pore, causing the conductance of the pore to return to its original value. This process repeated, resulting in stable oscillations of the ionic current. Although such oscillations might be useful in fluidic logic circuits, few conditions capable of generating oscillations in ionic currents have been reported. The frequency and amplitude of oscillations could be tuned by changing the concentration of the precipitating molecule, the pH of the electrolyte, and the applied potential bias. In addition to generating oscillations, nanopores that separate two different solutions may be useful for monitoring and mediating chemical reactions in the mixing zone between two solutions.

Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors

Small RNA molecules have an important role in gene regulation and RNA silencing therapy, but it is challenging to detect these molecules without the use of time-consuming radioactive labelling assays or error-prone amplification methods. Here, we present a platform for the rapid electronic detection of probe-hybridized microRNAs from cellular RNA. In this platform, a target microRNA is first hybridized to a probe. This probe:microRNA duplex is then enriched through binding to the viral protein p19. Finally, the abundance of the duplex is quantified using a nanopore. Reducing the thickness of the membrane containing the nanopore to 6 nm leads to increased signal amplitudes from biomolecules, and reducing the diameter of the nanopore to 3 nm allows the detection and discrimination of small nucleic acids based on differences in their physical dimensions. We demonstrate the potential of this approach by detecting picogram levels of a liver-specific miRNA from rat liver RNA.

Robust properties of membrane-embedded connector channel of bacterial virus phi29 DNA packaging motor

Biological systems contain highly-ordered macromolecular structures with diverse functions, inspiring their utilization in nanotechnology. A motor allows linear dsDNA viruses to package their genome into a preformed procapsid. The central component of the motor is the portal connector that acts as a pathway for the translocation of dsDNA. The elegant design of the connector and its channel motivates its application as an artificial nanopore (Nature Nanotechnology, 4, 765-772). Herein, we demonstrate the robust characteristics of the connector of the bacteriophage phi29 DNA packaging motor by single pore electrophysiological assays. The conductance of each pore is almost identical and is perfectly linear with respect to the applied voltage. Numerous transient current blockade events induced by dsDNA are consistent with the dimensions of the channel and dsDNA. Furthermore, the connector channel is stable under a wide range of experimental conditions including high salt and pH 2-12. The robust properties of the connector nanopore made it possible to develop a simple reproducible approach for connector quantification. The precise number of connectors in each sheet of the membrane was simply derived from the slopes of the plot of voltage against current. Such quantifications led to a reliable real time counting of DNA passing through the channel. The fingerprint of DNA translocation in this system has provided a new tool for future biophysical and physicochemical characterizations of DNA transportation, motion, and packaging.

Recent advances in the development of nucleic acid diagnostics

Since the early 1970s, the use of nucleic acid sequences for specific diagnostic applications has followed a somewhat linear pattern of development. Early methods for restriction enzyme digestion, as well as reverse transcription, were followed in the late 1970s by Southern, northern and dot blotting, as well as DNA sequencing. In 1985, the description of PCR and the routine laboratory manipulation of sufficient quantities of DNA for diagnostics, resulted in the exponential growth of molecular biology. Subsequently, alternative DNA and RNA amplification protocols followed. The last 10 years have seen the second explosion in molecular biology with the development of real-time quantitative PCR and oligonucleotide microarrays. This advancement continues with the development of methods for 'direct' nucleic acid target detection from samples without in vitro amplification, and enhanced transduction elements for improved sensitivity of nucleic acid detection. In this article, we will describe the current state of the art in nucleic acid diagnostics, the use of nucleic acid-based diagnostics in clinical practice and the emerging technologies in the field. Finally, we will describe future trends and expected advances in the field.

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.

Sub-10-nm nanochannels by self-sealing and self-limiting atomic layer deposition

We report on a novel fabrication method of a nanochannel ionic field effect transistor (IFET) structure with sub-10-nm dimensions. A self-sealing and self-limiting atomic layer deposition (ALD) facilitates the fabrication of lateral type nanochannels smaller than the e-beam or optical lithographic limits. Using highly conformal ALD film structures, including TiO(2), TiO(2)/TiN, and Al(2)O(3)/Ru, we have fabricated lateral sub-10-nm nanochannels with good control over channel diameter. Nanochannels surrounded by core/shell (high-k dielectric/metal) layers give rise to all-around-gating IFETs, an important functional element in an electrofluidic-based circuit system.