Nanopore sequencing technology: nanopore preparations

ATP-modulated ionic transport through synthetic nanochannels

Here, we demonstrate an anion controlled molecular gate based on synthetic ion channels modified with polyethyleneimine. For single conical nanochannels, addition of ATP leads to significant decrease in the rectified ion flux, representing the closure of the ionic gate. Complementary experiments performed with nanoporous membranes show that the flux of charged dye (NDS(2-)) through a cylindrical nanochannel array diminishes by the co-addition of ATP in the analyte solution.

Stochastic nanopore sensors for the detection of terrorist agents: current status and challenges

Nanopore stochastic sensor works by monitoring the ionic current modulations induced by the passage of analytes of interest through a single pore, which can be obtained from a biological ion channel by self-assembly or artificially fabricated in a solid-state membrane. In this minireview, we overview the use of biological nanopores and artificial nanopores for the detection of terrorist agents including explosives, organophosphorus nerve agents, nitrogen mustards, organoarsenic compounds, toxins, and viruses. We also discuss the current challenge in the development of deployable nanopore sensors for real-world applications.

Applications of biological pores in nanomedicine, sensing, and nanoelectronics

Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated - often regulated - functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics.

Electrically facilitated translocations of proteins through silicon nitride nanopores: conjoint and competitive action of diffusion, electrophoresis, and electroosmosis

Solid-state nanopores bear great potential to be used to probe single proteins; however, the passage of proteins through nanopores was found to be complex, and unexpected translocation behavior with respect to the passage direction, rate, and duration was observed. Here we study the translocation of a model protein (avidin) through silicon nitride nanopores focusing on the electrokinetic effects that facilitate protein transport across the pore. The nanopore zeta potential zeta(pore) and the protein zeta potential zeta(protein) are measured independently as a function of solution pH. Our results reveal that electroosmotic transport may enhance or dominate and reverse electrophoretic transport in nanopores. The translocation behavior is rationalized by accounting for the charging states of the protein and the pore, respectively; the resulting translocation direction can be predicted according to the difference in zeta potentials, zeta(protein) - zeta(pore). When electrophoresis and electroosmosis cancel each other out, diffusion becomes an effective (and bias-independent) mechanism which facilitates protein transport across the pore at a significant rate.

Bacterial nanofluidic structures for medicine and engineering

Bacteria are microscopic, single-celled organisms that utilize a variety of nanofluidic structures. One of the best known and widely used nanofluidic structures that are derived from bacteria is the alpha-hemolysin pore. This pore, which self-assembles in lipid bilayers, has been used for a wide variety of sensing applications, most notably, DNA sensing. Synthetic pores drilled in a wide variety of materials, such as silicon nitride and polymers have been developed that use inspiration from the alpha-hemolysin pore. Higher-aspect-ratio nanofluidic structures, akin to nanotubes, are also synthesized by bacteria. Examples of such structures include those that are associated with bacterial transport apparatus, such as pili, and are used by bacteria to facilitate the transfer of genetic material from one bacterium to another. Flagella, and its associated structures, such as the rod and hook, are also tubular nanostructures, through which the protein, flagellin, travels to assemble the flagellum. Genetic engineering allows for the creation of modified bacterial nanopores and nanotubes that can be used for a variety of medical and engineering purposes.

Deciphering ionic current signatures of DNA transport through a nanopore

Within just a decade from the pioneering work demonstrating the utility of nanopores for molecular sensing, nanopores have emerged as versatile systems for single-molecule manipulation and analysis. In a typical setup, a gradient of the electrostatic potential captures charged solutes from the solution and forces them to move through a single nanopore, across an otherwise impermeable membrane. The ionic current blockades resulting from the presence of a solute in a nanopore can reveal the type of the solute, for example, the nucleotide makeup of a DNA strand. Despite great success, the microscopic mechanisms underlying the functionality of such stochastic sensors remain largely unknown, as it is not currently possible to characterize the microscopic conformations of single biomolecules directly in a nanopore and thereby unequivocally establish the causal relationship between the observables and the microscopic events. Such a relationship can be determined using molecular dynamics-a computational method that can accurately predict the time evolution of a molecular system starting from a given microscopic state. This article describes recent applications of this method to the process of DNA transport through biological and synthetic nanopores.

A long DNA segment in a linear nanoscale Paul trap

We study the dynamics of a linearly distributed line charge such as single stranded DNA (ssDNA) in a nanoscale, linear 2D Paul trap in vacuum. Using molecular dynamics simulations we show that a line charge can be trapped effectively in the trap for a well defined range of stability parameters. We investigated (i) a flexible bonded string of charged beads and (ii) a ssDNA polymer of variable length, for various trap parameters. A line charge undergoes oscillations or rotations as it moves, depending on its initial angle, the position of the center of mass and the velocity. The stability region for a strongly bonded line of charged beads is similar to that of a single ion with the same charge to mass ratio. Single stranded DNA as long as 40 nm does not fold or curl in the Paul trap, but could undergo rotations about the center of mass. However, we show that a stretching field in the axial direction can effectively prevent the rotations and increase the confinement stability.

Analysis of single nucleic acid molecules with protein nanopores

We describe the methods used in our laboratory for the analysis of single nucleic acid molecules with protein nanopores. The technical section is preceded by a review of the variety of experiments that can be done with protein nanopores. The end goal of much of this work is single-molecule DNA sequencing, although sequencing is not discussed explicitly here. The technical section covers the equipment required for nucleic acid analysis, the preparation and storage of the necessary materials, and aspects of signal processing and data analysis.

Translocation of single-stranded DNA through single-walled carbon nanotubes

We report the fabrication of devices in which one single-walled carbon nanotube spans a barrier between two fluid reservoirs, enabling direct electrical measurement of ion transport through the tube. A fraction of the tubes pass anomalously high ionic currents. Electrophoretic transport of small single-stranded DNA oligomers through these tubes is marked by large transient increases in ion current and was confirmed by polymerase chain reaction analysis. Each current pulse contains about 10(7) charges, an enormous amplification of the translocated charge. Carbon nanotubes simplify the construction of nanopores, permit new types of electrical measurements, and may open avenues for control of DNA translocation.

DNA strands from denatured duplexes are translocated through engineered protein nanopores at alkaline pH

Nanopores are under development for the detection of a variety of analytes and the investigation of chemical reactions at the single molecule level. In particular, the analysis of nucleic acid molecules is under intense investigation, including the development of systems for rapid, low-cost DNA sequencing. Here, we show that DNA can be translocated through an engineered alphaHL protein pore at pH 11.7, a value at which dsDNA is denatured. Therefore, the alphaHL pore is sufficiently stable to entertain the possibility of direct nanopore sequencing of genomic dsDNA samples, which are more readily obtained and handled than ssDNA.

Membrane proteins in nanotechnology

Integral membrane proteins are important biological macromolecules with structural features and functionalities that make them attractive targets for nanotechnology. I provide here a broad review of current activity in nanotechnology related to membrane proteins, including their application as nanoscale sensors, switches, components of optical devices and as templates for self-assembled arrays.

Translational nanomedicine: status assessment and opportunities

Nano-enabled technologies hold great promise for medicine and health. The rapid progress by the physical sciences/engineering communities in synthesizing nanostructures and characterizing their properties must be rapidly exploited in medicine and health toward reducing mortality rate, morbidity an illness imposes on a patient, disease prevalence, and general societal burden. A National Science Foundation-funded workshop, "Re-Engineering Basic and Clinical Research to Catalyze Translational Nanoscience," was held 16-19 March 2008 at the University of Southern California. Based on that workshop and literature review, this article briefly explores scientific, economic, and societal drivers for nanomedicine initiatives; examines the science, engineering, and medical research needs; succinctly reviews the US federal investment directly germane to medicine and health, with brief mention of the European Union (EU) effort; and presents recommendations to accelerate the translation of nano-enabled technologies from laboratory discovery into clinical practice.

FROM THE CLINICAL EDITOR

An excellent review paper based on the NSF funded workshop "Re-Engineering Basic and Clinical Research to Catalyze Translational Nanoscience" (16-19 March 2008) and extensive literature search, this paper briefly explores the current state and future perspectives of nanomedicine.

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.

Translocation through the nuclear pore: Kaps pave the way

Transport through the nuclear pore complex (NPC), a keystone of the eukaryotic building plan, is known to involve a large channel and an abundance of phenylalanine-glycine (FG) protein domains serving as binding sites for soluble nuclear transport receptors and their cargo complexes. However, the conformation of the FG domains in vivo, their arrangement in relation to the transport channel and their function(s) in transport are still vividly debated. Here, we revisit a number of representative transport models-specifically Brownian affinity gating, selective phase gating, reversible FG domain collapse, and reduction of dimensionality (ROD)-in the light of new data obtained by optical single transporter recording, optical superresolution microscopy, artificial nanopores, and many other techniques. The analysis suggests that a properly adapted, simplified version of the ROD model accounts well for the available data. This has implications for nucleocytoplasmic transport in general.

Interrogating single proteins through nanopores: challenges and opportunities

A single nanopore represents an amazingly versatile single-molecule probe that can be employed to reveal several important features of polypeptides, such as their folding state, backbone flexibility, mechanical stability, binding affinity to other interacting ligands and enzymatic activity. Moreover, groundwork in this area using engineered protein nanopores has demonstrated new opportunities for discovering the biophysical rules that govern the transport of proteins through transmembrane protein pores. In this review, I summarize the current knowledge in the field and discuss how nanopore probe techniques will provide a new generation of research tools in nanomedicine for quantitatively examining the details of complex recognition and, furthermore, will represent a crucial step in designing other pore-based nanostructures and high-throughput devices for molecular biomedical diagnosis.

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.

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.

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.

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.

Fabrication and functionalization of single asymmetric nanochannels for electrostatic/hydrophobic association of protein molecules

We have developed a facile and reproducible method for surfactant-controlled track-etching and chemical functionalization of single asymmetric nanochannels in PET (polyethylene terephthalate) membranes. Carboxyl groups present on the channel surface were converted into pentafluorophenyl esters using EDC/PFP (N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride/pentafluorophenol) coupling chemistry. The resulting amine-reactive esters were further covalently coupled with ethylenediamine or propylamine in order to manipulate the charge polarity and hydrophilicity of the nanochannels, respectively. Characterization of the modified channels was done by measuring their current-voltage (I-V) curves as well as their permselectivity before and after the chemical modification. The electrostatic/hydrophobic association of bovine serum albumin on the channel surface was observed through the change in rectification behaviour upon the variation of pH values.

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.

A molecular dynamics simulation study on trapping ions in a nanoscale Paul trap

We found by molecular dynamics simulations that a low energy ion can be trapped effectively in a nanoscale Paul trap in both vacuum and aqueous environments when appropriate AC/DC electric fields are applied to the system. Using the negatively charged chlorine ion as an example, we show that the trapped ion oscillates around the center of the nanotrap with an amplitude dependent on the parameters of the system and applied voltages. Successful trapping of the ion within nanoseconds requires an electric bias of GHz frequency, in the range of hundreds of mV. The oscillations are damped in the aqueous environment, but polarization of water molecules requires the application of a higher voltage bias to reach improved stability of the trapping. Application of a supplemental DC driving field along the trap axis can effectively drive the ion off the trap center and out of the trap, opening up the possibility of studying DNA and other charged molecules using embedded probes while achieving a full control of their translocation and localization in the trap.

Outer membrane protein G: Engineering a quiet pore for biosensing

Bacterial outer membrane porins have a robust beta-barrel structure and therefore show potential for use as stochastic sensors based on single-molecule detection. The monomeric porin OmpG is especially attractive compared with multisubunit proteins because appropriate modifications of the pore can be easily achieved by mutagenesis. However, the gating of OmpG causes transient current blockades in single-channel recordings that would interfere with analyte detection. To eliminate this spontaneous gating activity, we used molecular dynamics simulations to identify regions of OmpG implicated in the gating. Based on our findings, two approaches were used to enhance the stability of the open conformation by site-directed mutagenesis. First, the mobility of loop 6 was reduced by introducing a disulfide bond between the extracellular ends of strands beta12 and beta13. Second, the interstrand hydrogen bonding between strands beta11 and beta12 was optimized by deletion of residue D215. The OmpG porin with both stabilizing mutations exhibited a 95% reduction in gating activity. We used this mutant for the detection of adenosine diphosphate at the single-molecule level, after equipping the porin with a cyclodextrin molecular adapter, thereby demonstrating its potential for use in stochastic sensing applications.

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.

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.