Ion-beam sculpting at nanometre length scales

Electrophoretic force on a protein-coated DNA molecule in a solid-state nanopore

Using solid-state nanopores with optical tweezers, we perform force spectroscopy on DNA molecules that are coated with RecA proteins. We observe that the electrophoretic force is 2-4 times larger for RecA-DNA filaments than for uncoated DNA molecules and that this force increases at lower salt concentrations. The data demonstrate the efficacy of solid-state nanopores for locally probing the forces on DNA-bound proteins. Our results are described quantitatively by a model that treats the electrophoretic and hydrodynamic forces. The conductance steps that occur when RecA-DNA enters the nanopore change from conductance decreases at high salt to conductance increases at low salt, which allows the apparent charge of the RecA-DNA filament to be extracted. The combination of conductance measurements with local force spectroscopy increases the potential for future solid-state nanopore screening devices.

Versatile ultrathin nanoporous silicon nitride membranes

Single- and multiple-nanopore membranes are both highly interesting for biosensing and separation processes, as well as their ability to mimic biological membranes. The density of pores, their shape, and their surface chemistry are the key factors that determine membrane transport and separation capabilities. Here, we report silicon nitride (SiN) membranes with fully controlled porosity, pore geometry, and pore surface chemistry. An ultrathin freestanding SiN platform is described with conical or double-conical nanopores of diameters as small as several nanometers, prepared by the track-etching technique. This technique allows the membrane porosity to be tuned from one to billions of pores per square centimeter. We demonstrate the separation capabilities of these membranes by discrimination of dye and protein molecules based on their charge and size. This separation process is based on an electrostatic mechanism and operates in physiological electrolyte conditions. As we have also shown, the separation capabilities can be tuned by chemically modifying the pore walls. Compared with typical membranes with cylindrical pores, the conical and double-conical pores reported here allow for higher fluxes, a critical advantage in separation applications. In addition, the conical pore shape results in a shorter effective length, which gives advantages for single biomolecule detection applications such as nanopore-based DNA analysis.

Shadow overlap ion-beam lithography for nanoarchitectures

Precisely constructed nanoscale devices and nanoarchitectures with high spatial resolution are critically needed for applications in high-speed electronics, high-density memory, efficient solar cells, optoelectronics, plasmonics, optical antennas, chemical sensors, biological sensors, and nanospectroscopic imaging. Current methods of classical optical lithography are limited by the diffraction effect of light for nanolithography, and the state of art of e-beam or focused ion beam lithography limit the throughput and further reduction less than few nanometers for large-area batch fabrication. However, these limits can be surpassed surprisingly by utilizing the overlap of two shadow images. Here we present shadow overlap of ion-beam lithography (SOIL), which can combine the advantages of parallel processing, tunable capability of geometries, cost-effective method, and high spatial resolution nanofabrication technique. The SOIL method relies on the overlap of shadows created by the directional metal deposition and etching angles on prepatterned structures. Consequently, highly tunable patterns can be obtained. As examples, unprecedented nanoarchitectures for optical antennas are demonstrated by SOIL. We expect that SOIL can have a significant impact not only on nanoscale devices, but also large-scale (i.e., micro and macro) three-dimensional innovative lithography.

Capturing single molecules of immunoglobulin and ricin with an aptamer-encoded glass nanopore

Nanopore-based single-molecule biosensors have been extensively studied. Protein pores that have receptors attached to them are target-selective, but their real-time applications are limited by the fragility of the lipid membrane into which the protein pores are embedded. Synthetic nanopores are more stable and provide flexible pore sizes, but the selectivity is low when detecting in the translocation mode. In spite of modifications with probing molecules, such as antibodies, to potentiate specific targeting, these nanopores fail to bind individual target molecules. Distinguishing between binding and translocation blocks remains unsolved. Here, we propose an aptamer-encoded nanopore that overcomes these challenges. Aptamers are well-known probing oligonucleotides that have high sensitivity and selectivity. In contrast to antibodies, aptamers are much smaller than their targets, rendering target blockades in the nanopore much more distinguishable. We used aptamer-encoded nanopores to detect single molecules of immunoglobulin E and the bioterrorist agent ricin, sequentially captured by the immobilized aptamer in the sensing zone of the pore. The functional nanopore also probed sequence-dependent aptamer-protein interactions. These findings will facilitate the development of a universal nanopore for multitarget detection.

Ionic current through a nanopore three nanometers in diameter

Ionic current through a 3 nm in diameter nanopore has been investigated using molecular dynamics. Results indicate that the ionic current increases linearly as the electrolyte concentration increases from 0.4 to 0.9 M, beyond which the ionic current increases at a slower rate. In contradiction to the expectation that higher surface charge density will lead to more ions in the nanopore, and therefore, higher ionic current, the ionic current shows an increase-decrease profile as the surface charge density increases. These unusual observations are attributed to the fact that ions close to the wall experience large viscous force, leading to low mobility.

Single-molecule protein unfolding in solid state nanopores

We use single silicon nitride nanopores to study folded, partially folded, and unfolded single proteins by measuring their excluded volumes. The DNA-calibrated translocation signals of beta-lactoglobulin and histidine-containing phosphocarrier protein match quantitatively with that predicted by a simple sum of the partial volumes of the amino acids in the polypeptide segment inside the pore when translocation stalls due to the primary charge sequence. Our analysis suggests that the majority of the protein molecules were linear or looped during translocation and that the electrical forces present under physiologically relevant potentials can unfold proteins. Our results show that the nanopore translocation signals are sensitive enough to distinguish the folding state of a protein and distinguish between proteins based on the excluded volume of a local segment of the polypeptide chain that transiently stalls in the nanopore due to the primary sequence of charges.

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.

Selective sputtering and atomic resolution imaging of atomically thin boron nitride membranes

We report on the preparation, atomic resolution imaging, and element selective damage mechanism in atomically thin boron nitride membranes. Flakes of less than 10 layers are prepared by mechanical cleavage and are thinned down to single layers in a high-energy electron beam. At our beam energies, we observe a highly selective sputtering of only one of the elements and predominantly at the exit surface of the specimen, and then subsequent removal of atoms next to a defect. Triangle-shaped holes appear in accordance with the crystallographic orientation of each layer. Defects are compared to those observed in graphene membranes. The observation of clean single-layer membranes shows that hexagonal boron nitride is a further material (in addition to graphene) that can exist in a quasi-two-dimensional allotrope without the need for a substrate.

Probing surface charge fluctuations with solid-state nanopores

We identify a contribution to the ionic current noise spectrum in solid-state nanopores that exceeds all other noise sources in the frequency band 0.1-10 kHz. Experimental studies of the dependence of this excess noise on pH and electrolyte concentration indicate that the noise arises from surface charge fluctuations. A quantitative model based on surface functional group protonization predicts the observed behaviors and allows us to locally measure protonization reaction rates. This noise can be minimized by operating the nanopore at a deliberately chosen pH.

Mapping the position of DNA polymerase-bound DNA templates in a nanopore at 5 A resolution

DNA polymerases are molecular motors that catalyze template-dependent DNA replication, advancing along template DNA by one nucleotide with each catalytic cycle. Nanopore-based measurements have emerged as a single molecule technique for the study of these enzymes. Using the alpha-hemolysin nanopore, we determined the position of DNA templates bearing inserts of abasic (1',2'-dideoxy) residues, bound to the Klenow fragment of Escherichia coli DNA polymerase I (KF) or to bacteriophage T7 DNA polymerase. Hundreds of individual polymerase complexes were analyzed at 5 A precision within minutes. We generated a map of current amplitudes for DNA-KF-deoxynucleoside triphosphate (dNTP) ternary complexes, using a series of templates bearing blocks of three abasic residues that were displaced by approximately 5 A in the nanopore lumen. Plotted as a function of the distance of the abasic insert from n = 0 in the active site of the enzyme held atop the pore, this map has a single peak. The map is similar when the primer length, the DNA sequences flanking the abasic insert, and the DNA sequences in the vicinity of the KF active site are varied. Primer extension catalyzed by KF using a three abasic template in the presence of a mixture of dNTPs and 2',3'-dideoxynucleoside triphosphates resulted in a ladder of ternary complexes with discrete amplitudes that closely corresponded to this map. An ionic current map measured in the presence of 0.15 M KCl mirrored the map obtained with 0.3 M KCl, permitting experiments with a broader range of mesophilic DNA and RNA processing enzymes. We used the abasic templates to show that capture of complexes with the KF homologue, T7 DNA polymerase, yields an amplitude map nearly indistinguishable from the KF map.

Biosensing with nanofluidic diodes

Recently reported nanofluidic diodes with highly nonlinear current-voltage characteristics offer a unique possibility to construct different biosensors. These sensors are based on local changes of the surface charge on walls of single conical nanopores induced by binding of an analyte. The analyte binding can be detected as a change of the ion-current rectification of single nanopores defined as a ratio of currents for voltages of one polarity, and currents for voltages of the opposite polarity. In this article, we provided both modeling and experimental studies of various biosensing routes based on monitoring changes of the rectification degree in nanofluidic diodes used as a biosensing platform. A prototype of a sensor for the capsular poly gamma-D-glutamic acid (gammaDPGA) from Bacillus anthracis is presented. The nanopore used for the sensing was locally modified with the monoclonal antibody for gammaDPGA. The proof of principle of the rectification degree-based sensing was further shown by preparation of sensors for avidin and streptavidin. Our devices also allowed for determination of the isoelectric point of the minute amounts of proteins immobilized on the surface.

The controlled fabrication of nanopores by focused electron-beam-induced etching

The fabrication of nanometric holes within thin silicon-based membranes is of great importance for various nanotechnology applications. The preparation of such holes with accurate control over their size and shape is, thus, gaining a lot of interest. In this work we demonstrate the use of a focused electron-beam-induced etching (FEBIE) process as a promising tool for the fabrication of such nanopores in silicon nitride membranes and study the process parameters. The reduction of silicon nitride by the electron beam followed by chemical etching of the residual elemental silicon results in a linear dependence of pore diameter on electron beam exposure time, enabling accurate control of nanopore size in the range of 17-200 nm in diameter. An optimal pressure of 5.3 x 10(-6) Torr for the production of smaller pores with faster process rates, as a result of mass transport effects, was found. The pore formation process is also shown to be dependent on the details of the pulsed process cycle, which control the rate of the pore extension, and its minimal and maximal size. Our results suggest that the FEBIE process may play a key role in the fabrication of nanopores for future devices both in sensing and nano-electronics applications.

Nanolithography based on an atom pinhole camera

In modern experimental physics the pinhole camera is used when the creation of a focusing element (lens) is difficult. We have experimentally realized a method of image construction in atom optics, based on the idea of an optical pinhole camera. With the use of an atom pinhole camera we have built an array of identical arbitrary-shaped atomic nanostructures with the minimum size of an individual nanostructure element down to 30 nm on an Si surface. The possibility of 30 nm lithography by means of atoms, molecules and clusters has been shown.

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.

Ionic field effect transistors with sub-10 nm multiple nanopores

We report a new method to fabricate electrode-embedded multiple nanopore structures with sub-10 nm diameter, which is designed for electrofluidic applications such as ionic field effect transistors. Our method involves patterning pore structures on membranes using e-beam lithography and shrinking the pore diameter by a self-limiting atomic layer deposition process. We demonstrate that 70-80 nm diameter pores can be shrunk down to sub-10 nm diameter and that the ionic transport of KCl electrolyte can be efficiently manipulated by the embedded electrode within the membrane.

Nanofluidic structures with complex three-dimensional surfaces

Nanofluidic devices have typically explored a design space of patterns limited by a single nanoscale structure depth. A method is presented here for fabricating nanofluidic structures with complex three-dimensional (3D) surfaces, utilizing a single layer of grayscale photolithography and standard integrated circuit manufacturing tools. This method is applied to construct nanofluidic devices with numerous (30) structure depths controlled from approximately 10 to approximately 620 nm with an average standard deviation of <10 nm over distances of >1 cm. A prototype 3D nanofluidic device is demonstrated that implements size exclusion of rigid nanoparticles and variable nanoscale confinement and deformation of biomolecules.

Polymer translocation in a double-force arrangement

Using Langevin dynamics simulations, we investigate the translocation dynamics of an externally driven polymer chain through a nanopore, where a pulling force F is exerted on the first monomer whilst there is an opposing force F(E) < F within the pore. Such a double-force arrangement has been proposed recently to allow better dynamical control of the translocation process in order to sequence biopolymers. We find that in the double-force arrangement translocation becomes slower as compared to the case under a single monomer pulling force of magnitude F-F(E), but scaling of the translocation time as a function of the chain length tau approximately N2 does not change. The waiting time tau(m) for monomer m to exit the pore is found to be a monotonically increasing function of the bead number almost until m approximately N , which indicates relatively well-defined slowing down and control of the chain velocity during translocation. We also study the waiting time distributions for the beads in the chain, and characterize in detail fluctuations in the bead positions and their transverse position coordinates during translocation. These data should be useful in estimating position-dependent sequencing errors in double-force experiments.

Transverse field effects on DNA-sized particle dynamics

We report the development of microfluidics-integrated mechanically controllable break junction device and its applications to electrical characterizations of DNA-sized particle dynamics in a microfluidic channel. It is found that the electrostatic electrode-particle interaction slows down the particle flow through the electrode nanogaps. The present results suggest the useful capability of transverse electric field for controlling DNA translocations through a nanopore.

Biosensing and supramolecular bioconjugation in single conical polymer nanochannels. Facile incorporation of biorecognition elements into nanoconfined geometries

There is a growing quest for tailorable nanochannels or nanopores having dimensions comparable to the size of biological molecules and mimicking the function of biological ion channels. This interest is based on the use of nanochannels as extremely sensitive single molecule biosensors. The biosensing capabilities of these nanochannels depend sensitively on the surface characteristics of their inner walls to achieve the desired functionality of the biomimetic system. Nanoscale control over the surface properties of the nanochannel plays a crucial role in the biosensing performance due to the chemical groups incorporated on the inner channel walls that act as binding sites for different analytes and interact with molecules passing through the channel. Here we report a new approach to incorporate biosensing elements into polymer nanochannels by using electrostatic self-assembly. We describe a facile strategy based on the use of bifunctional macromolecular ligands to electrostatically assemble biorecongnition sites into the nanochannel wall, which can then be used as recognition elements for constructing a nanobiosensor. The experimental results demonstrate that the ligand-functionalized nanochannels are very stable and the biorecognition event (protein conjugation) does not promote the removal of the ligands from the channel surface. In addition, control experiments indicated that the electrostatically assembled nanochannel surface displays good biospecificity and nonfouling properties. Then, we demonstrate that this approach also enables the creation of supramolecular multilayered structures inside the nanopore that are stabilized by strong ligand-receptor interactions. We envision that the formation of multilayered supramolecular assemblies inside solid-state nanochannels will play a key role in the further expansion of the toolbox called "soft nanotechnology", as well as in the construction of new multifunctional biomimetic systems.

Molecular simulation of ion transport in silica nanopores

Ion distribution and transport of KCl aqueous solutions at the junction of hydrophobic and hydrophilic regions inside silica nanopores were studied by using two kinds of molecular simulation: grand canonical Monte Carlo (GCMC) simulations and nonequilibrium molecular dynamics (NEMD) simulations. The nanopores were 2 nm diameter silica pores in which surface functional groups, -SiOH, had been modified by hydrophobic surface functional groups, -SiCH(3), within three different lengths along the pore direction (z-direction), L(z0) = 0, 2, and 4 nm. If L(z0) is long enough, water could not enter the hydrophobic region, but for all L(z0) studied here, water entered the hydrophobic region. When an external electric field was applied along the z-direction, ions could not pass through the hydrophobic region when the external electric field was less than a threshold level, E(0), whereas the ionic current increased relatively linearly with increasing electric field strength above E(0). In 2 nm diameter fluidic pores, the electrical potential barrier appeared at the junction between the hydrophilic and hydrophobic regions due to the difference in dipole moment of the surface functional groups, although the overall surface charge of the pore was neutral. This junction formed an electrical potential threshold, and the ionic current could be modulated by adjusting the external electric field.

Shrinking solid-state nanopores using electron-beam-induced deposition

Solid-state nanopores of only a few nanometres in size show a great potential for applications such as molecule detection and DNA sequencing. In most cases, the fabrication of such a nanopore requires the high energy beam of a transmission electron microscope (TEM) or focused ion beam (FIB) tool to drill or reshape a small hole in a freestanding membrane. Here, we present a novel method to reduce the size of existing nanopores using electron-beam-induced deposition (EBID) of carbon in a conventional scanning electron microscope (SEM). The existing nanopores are etched in a silicon membrane using anisotropic wet etching and can be shrunk down to a few nanometres using EBID. This paper discusses the parameters that influence the rate of shrinking and provides an insight into the underlying mechanism.

Nanoscale ripples on polymers created by a focused ion beam

We show that focused ion beam irradiation results in the creation of peculiar one- and two-dimensional nanoscale features on the surface of polyimide-a common polymer in electronics, large scale structures, and the automobile industry, as well as in biomedical applications. The role of ion beam incident angle, acceleration voltage, and fluence on the morphology of the structural features is systematically investigated, and insights into the mechanisms of formation of these nanoscale features are provided. Moreover, by using the maskless patterning method of the focused ion beam system, we have developed a robust technique for controlled modification of the polymeric surface. The technique, which is analogous to using a gray glass with varying darkness to control the radiation from the sun, but at a much smaller scale, enables the ion intensity and angle to be controlled at each surface point of the polymer, giving rise to structural surface features with desired shape and morphology.

Irradiation-induced shrinkage and expansion mechanisms of SiO2 circle membrane nanopores

20 nm diameter SiO(2) nanopore arrays on gradient-thickness membranes were formed by a focused electron beam with in situ transmission electron microscopy (TEM). Nanopore shrinkage was seen in nanopores on thicker membranes, with the rate of diameter change remaining constant during the shrinkage process. In contrast, pore expansion was observed in thinner membranes, with the expansion rate being constant at the initial stage but with a slight increase at the later stage. The geometry model of shrinkage and expansion of the nanopores in relation to the electron irradiation time was investigated by utilizing the TEM tilting method.

Fast single-step fabrication of nanopores

We report a new method for the fabrication of sub-10 nm nanopores in a fast single process step. The pore formation is accomplished by exploiting the competition between sputtering and deposition in ion-beam-induced deposition (IBID) on a thin membrane. The pore diameter can be controlled by adjusting the ion beam and gas exposure conditions. The pore diameter is well below the limit that can be achieved by focused ion beam (FIB) milling alone. There is no need of preparation and successive treatments. Apart from simplicity and speed, this method offers an additional advantage of a broad choice of material and thickness of the deposit and the membrane.

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.

Microscopic mechanics of hairpin DNA translocation through synthetic nanopores

Nanoscale pores have proved useful as a means to assay DNA and are actively being developed as the basis of genome sequencing methods. Hairpin DNA (hpDNA), having both double-helical and overhanging coil portions, can be trapped in a nanopore, giving ample time to execute a sequence measurement. In this article, we provide a detailed account of hpDNA interaction with a synthetic nanopore obtained through extensive all-atom molecular dynamics simulations. For synthetic pores with minimum diameters from 1.3 to 2.2 nm, we find that hpDNA can translocate by three modes: unzipping of the double helix and--in two distinct orientations--stretching/distortion of the double helix. Furthermore, each of these modes can be selected by an appropriate choice of the pore size and voltage applied transverse to the membrane. We demonstrate that the presence of hpDNA can dramatically alter the distribution of ions within the pore, substantially affecting the ionic current through it. In experiments and simulations, the ionic current relative to that in the absence of DNA can drop below 10% and rise beyond 200%. Simulations associate the former with the double helix occupying the constriction and the latter with accumulation of DNA that has passed through the constriction.

Nanofluidic channel fabrication and manipulation of DNA molecules

Confining DNA molecules in a nanofluidic channel, particularly in channels with cross sections comparable to the persistence length of the DNA molecule (about 50 nm), allows the discovery of new biophysical phenomena. This sub-100 nm nanofluidic channel can be used as a novel platform to study and analyze the static as well as the dynamic properties of single DNA molecules, and can be integrated into a biochip to investigate the interactions between protein and DNA molecules. For instance, nanofluidic channel arrays that have widths of approximately 40 nm, depths of 60 nm, and lengths of 50 mum are created rapidly and exactly by a focused-ion beam milling instrument on a silicon nitride film; and the open channels are sealed with anodic bonding technology. Subsequently, lambda phage DNA (lambda-DNA; stained with the fluorescent dye, YOYO-1) molecules are introduced into these nanoconduits by capillary force. The movements of the DNA molecules, e.g. stretching, recoiling, and transporting along channels, are studied with fluorescence microscopy.

Solid-state nanopore for detecting individual biopolymers

Solid-state nanopores have been fabricated and used to characterize single DNA and protein molecules. Here we describe the details on how these nanopores were fabricated and characterized, the nanopore sensing system setup, and protocols of using these nanopores to characterize DNA and protein molecules.

Molecular control of ionic conduction in polymer nanopores

Polymeric nanopores show unique transport properties and have attracted a great deal of scientific interest as a test system to study ionic and molecular transport at the nanoscale. By means of all-atom molecular dynamics, we simulated the ion dynamics inside polymeric polyethylene terephthalate nanopores. For this purpose, we established a protocol to assemble atomic models of polymeric material into which we sculpted a nanopore model with the key features of experimental devices, namely a conical geometry and a negative surface charge density. Molecular dynamics simulations of ion currents through the pore show that the protonation state of the carboxyl group of exposed residues have a considerable effect on ion selectivity, by affecting ionic densities and electrostatic potentials inside the nanopores. The role of high concentrations of Ca2+ ions was investigated in detail.

Method of creating a nanopore-terminated probe for single-molecule enantiomer discrimination

Nanopores are increasingly utilized as tools for single-molecule detection in biotechnology. Many nanopores are fabricated through procedures that require special materials, expensive facilities and experienced operators, which limit their usefulness on a wider scale. We have developed a simple method of fabricating a robust, low-noise nanopore by externally penetrating a nanocavity enclosed in the terminal of a capillary pipet. The nanocavity was shown to have a pore size on the scale of a single molecule, verified by translocation of molecules of known sizes, including double-stranded DNA (2 nm), gold nanoparticles (10 nm), and ring-shaped cyclodextrin (1.5 nm). The small pore size allows entrapment of a single cyclodextrin molecule. The glass nanopore with a trapped cyclodextrin proves useful in single-molecule discrimination of chiral enantiomers.

Single-molecule DNA detection with an engineered MspA protein nanopore

Nanopores hold great promise as single-molecule analytical devices and biophysical model systems because the ionic current blockades they produce contain information about the identity, concentration, structure, and dynamics of target molecules. The porin MspA of Mycobacterium smegmatis has remarkable stability against environmental stresses and can be rationally modified based on its crystal structure. Further, MspA has a short and narrow channel constriction that is promising for DNA sequencing because it may enable improved characterization of short segments of a ssDNA molecule that is threaded through the pore. By eliminating the negative charge in the channel constriction, we designed and constructed an MspA mutant capable of electronically detecting and characterizing single molecules of ssDNA as they are electrophoretically driven through the pore. A second mutant with additional exchanges of negatively-charged residues for positively-charged residues in the vestibule region exhibited a factor of approximately 20 higher interaction rates, required only half as much voltage to observe interaction, and allowed ssDNA to reside in the vestibule approximately 100 times longer than the first mutant. Our results introduce MspA as a nanopore for nucleic acid analysis and highlight its potential as an engineerable platform for single-molecule detection and characterization applications.

Stochastic sensing of biomolecules in a nanopore sensor array

In this study, we demonstrate that a pattern-recognition stochastic sensor can be constructed by employing an array of protein pores modified with a variety of non-covalent bonding sites as effective sensing elements. The collective responses of each of the individual component nanopores to a compound produce diagnostic patterns characterized by event dwell time, amplitude, and voltage dependence, which can independently or collectively serve as (an) analyte signature(s). With an increase in the dimensionality of the signal, the nanopore sensor array provides enhanced resolution for the differentiation of analytes compared to a single-pore configuration. This allows identification of a target analyte from a mixture or the potential for simultaneous detection. The pattern-recognition nanopore method is envisaged for further development as a miniaturized and automated sensing technique, which could find potential use as a laboratory or clinical tool for routine sensor applications, including environmental monitoring, drug discovery, medical diagnosis, and homeland security.

Enhanced translocation of single DNA molecules through alpha-hemolysin nanopores by manipulation of internal charge

Both protein and solid-state nanopores are under intense investigation for the analysis of nucleic acids. A crucial advantage of protein nanopores is that site-directed mutagenesis permits precise tuning of their properties. Here, by augmenting the internal positive charge within the alpha-hemolysin pore and varying its distribution, we increase the frequency of translocation of a 92-nt single-stranded DNA through the pore at +120 mV by approximately 10-fold over the wild-type protein and dramatically lower the voltage threshold at which translocation occurs, e.g., by 50 mV for 1 event.s(-1).muM(-1). Further, events in which DNA enters the pore, but is not immediately translocated, are almost eliminated. These experiments provide a basis for improved nucleic acid analysis with protein nanopores, which might be translated to solid-state nanopores by using chemical surface modification.

Translocation dynamics with attractive nanopore-polymer interactions

Using Langevin dynamics simulations, we investigate the influence of polymer-pore interactions on the dynamics of biopolymer translocation through nanopores. We find that an attractive interaction can significantly change the translocation dynamics. This can be understood by examining the three components of the total translocation time tau approximately tau1+tau2+tau3 corresponding to the initial filling of the pore, transfer of polymer from the cis side to the trans side, and emptying of the pore, respectively. We find that the dynamics for the last process of emptying of the pore changes from nonactivated to activated in nature as the strength of the attractive interaction increases, and tau3 becomes the dominant contribution to the total translocation time for strong attraction. This leads to nonuniversal dependence of tau as a function of driving force and chain length. Our results are in good agreement with recent experimental findings, and provide a plausible explanation for the different scaling behavior observed in solid state nanopores vs that for the natural alpha-hemolysin channel.

Resistive-pulse detection of short dsDNAs using a chemically functionalized conical nanopore sensor

Aims: To develop nanopore resistive-pulse sensors for the detection of short (50 base-pair [bp] and 100 bp) DNAs. Materials & methods: Conically shaped nanopores were chemical etched into polyethylene terphthalate membranes. The as-etched membrane had anionic carboxylate sites on the pore walls. Neutral and hydrophilic ethanolamine functional groups were attached to these carboxylate sites using well-established EDC (1-ethyl-3-[3-dimethylaminopropyl] carbodiimide hydrochloride) chemistry. Results & discussion: The ethanolamine-functionalized pores were used to detect 50 and 100 bp DNAs via the resistive-pulse method. The resistive-pulse signature produced by the 50 bp DNA could be distinguished from that of the 100 bp DNA with these sensors. Conclusions: Attachment of ethanolamine to the carboxylate groups on the pore wall lowered the anionic charge density on the wall. This mitigated the problem of electrostatic rejection of the anionic DNAs from the pore and enabled the detection of these DNA analytes.

Dynamics of DNA translocation through an attractive nanopore

We investigate the dynamics of single-stranded DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions to study how the translocation dynamics depend on the details of the DNA sequences. We consider a coarse-grained model of DNA built from two bases A and C, having different base-pore interactions, e.g., a strong (weak) attractive force between the pore and the base A (C) inside the pore. From a series of studies on hetero-DNAs with repeat units AmCn, we find that the translocation time decreases exponentially as a function of the volume fraction fC of the base C. For longer A sequences with fC<or=0.5, the translocation time strongly depends on the orientation of DNA, namely which base enters the pore first. Our studies clearly demonstrate that for a DNA of certain length N with repeat units AmCn, the pattern exhibited by the waiting times of the individual bases and their periodicity can unambiguously determine the values of m, n, and N, respectively. Therefore, a prospective experimental realization of this phenomenon may lead to fast and efficient sequence detection.

Multilayered semiconductor membranes for nanopore ionic conductance modulation

We explore the possibility of using thin layered semiconductor membranes for electrical control of the ion current flow through a nanopore, thereby operating like tunable ionic transistors. While single layer semiconductor membranes can be voltage tuned to operate as ionic filters or "switches", double layered membranes can rectify the ion current flowing through the nanopore in addition to ion filtering. Triple layer membranes exhibit enhanced functionality with characteristics similar to those of the single and double layer membranes in addition to bidirectional current blocking and switching, thereby operating similar to tunable ionic transistors.

Electromechanical unzipping of individual DNA molecules using synthetic sub-2 nm pores

Nanopores have recently emerged as high-throughput tools for probing and manipulating nucleic acid secondary structure at the single-molecule level. While most studies to date have utilized protein pores embedded in lipid bilayers, solid-state nanopores offer many practical advantages which greatly expand the range of applications in life sciences and biotechnology. Using sub-2 nm solid-state nanopores, we show for the first time that the unzipping kinetics of individual DNA duplexes can be probed by analyzing the dwell-time distributions. We performed high-bandwidth electrical measurements of DNA duplex unzipping as a function of their length, sequence, and temperature. We find that our longer duplexes (>10 bp) follow Arrhenius dependence on temperature, suggesting that unzipping can be approximated as a single-barrier crossing, but the unzipping kinetics of shorter duplexes do not involve a barrier, due to the strong biasing electrical force. Finally, we show that mismatches in the duplex affect unzipping times in a position-sensitive manner. Our results are a crucial step toward sequence variability detection and our single-molecule nanopore sequencing technology, which rely on parallel detection from nanopore arrays.

The potential and challenges of nanopore sequencing

A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of 'third generation' instruments that will sequence a diploid mammalian genome for approximately $1,000 in approximately 24 h.