Highly Sensitive, Mechanically Stable Nanopore Sensors for DNA Analysis

Sensing proteins through nanopores: fundamental to applications

Proteins subjected to an electric field and forced to pass through a nanopore induce blockades of ionic current that depend on the protein and nanopore characteristics and interactions between them. Recent advances in the analysis of these blockades have highlighted a variety of phenomena that can be used to study protein translocation and protein folding, to probe single-molecule catalytic reactions in order to obtain kinetic and thermodynamic information, and to detect protein-antibody complexes, proteins with DNA and RNA aptamers, and protein-pore interactions. Nanopore design is now well controlled, allowing the development of future biotechnologies and medicine applications.

Insertion kinetics of small nucleotides through single walled carbon nanotube

We report molecular dynamic simulations showing that a DNA molecule constituted by five unique bases can be spontaneously inserted into single walled carbon nanotube (SWCNT) in normal conditions (P, T and water environment) depending on the tube radius value. The van der Waals and electrostatic interactions play a central role for the rapid insertion process. Our study shows also that the Guanine molecule inserts the fastest compared to thymine, adenine and cytosine bases, respectively. The differences of insertion time could be exploited for applications concerning for example DNA sequencing.

Recent advances in nanopore sequencing

The prospect of nanopores as a next-generation sequencing platform has been a topic of growing interest and considerable government-sponsored research for more than a decade. Oxford Nanopore Technologies recently announced the first commercial nanopore sequencing devices, to be made available by the end of 2012, while other companies (Life, Roche, and IBM) are also pursuing nanopore sequencing approaches. In this paper, the state of the art in nanopore sequencing is reviewed, focusing on the most recent contributions that have or promise to have next-generation sequencing commercial potential. We consider also the scalability of the circuitry to support multichannel arrays of nanopores in future sequencing devices, which is critical to commercial viability.

Size-dependent evolution of graphene nanopores under thermal excitation

Graphene nanopores expand when pore diameter is larger than membrane thickness after heat treatment; otherwise, nanopore size shrinks. Such size-dependent evolutionary mechanism of nanopores is considered as thermal-induced migration of uncombined carbon atoms. The amount of carbon adatoms determines the extent of diameter change. This could provide an applicable strategy for nanopore fabrication.

Conductance-Based Determination of Solid-State Nanopore Size and Shape: An Exploration of Performance Limits

Knowledge of nanopore size and shape is critical for many implementations of these single-molecule sensing elements. Geometry determination by fitting the electrolyte-concentration-dependence of the conductance of surface-charged, solid-state nanopores has been proposed to replace demanding electron microscope-based methods. The functional form of the conductance poses challenges for this method by restricting the number of free parameters used to characterize the nanopore. We calculated the electrolyte-dependent conductance of nanopores with an exponential-cylindrical radial profile using three free geometric parameters; this profile, itself, could not be uniquely geometry-optimized by the conductance. Several different structurally simplified models, however, generated quantitative agreement with the conductance, but with errors exceeding 40% for estimates of key geometrical parameters. A tractable conical-cylindrical model afforded a good characterization of the nanopore size and shape, with errors of less than 1% for the limiting radius. Understanding these performance limits provides a basis for using and extending analytical nanopore conductance models.

Fabrication and characterization of solid-state nanopore arrays for high-throughput DNA sequencing

We report the fabrication and characterization of uniformly sized nanopore arrays, integrated into an optical detection system for high-throughput DNA sequencing applications. Nanopore arrays were fabricated using focused ion beam milling, followed by TiO(2) coating using atomic layer deposition. The TiO(2) layer decreases the initial pore diameter down to the sub-10 nm range, compatible with the requirements for nanopore-based sequencing using optical readout. We find that the TiO(2) layers produce a lower photoluminescence background as compared with the more widely used Al(2)O(3) coatings. The functionality of the nanopore array was demonstrated by the simultaneous optical detection of DNA-quantum dot conjugates, which were electro-kinetically driven through the nanopores. Our optical scheme employs total internal reflection fluorescence microscopy to illuminate a wide area of the TiO(2)-coated membrane. A highly parallel system for observing DNA capture events in a uniformly sized 6 × 6 nanopore array was experimentally realized.

Atomic layer deposition of nanostructured materials for energy and environmental applications

Atomic layer deposition (ALD) is a thin film technology that in the past two decades rapidly developed from a niche technology to an established method. It proved to be a key technology for the surface modification and the fabrication of complex nanostructured materials. In this Progress Report, after a short introduction to ALD and its chemistry, the versatility of the technique for the fabrication of novel functional materials will be discussed. Selected examples, focused on its use for the engineering of nanostructures targeting applications in energy conversion and storage, and on environmental issues, will be discussed. Finally, the challenges that ALD is now facing in terms of materials fabrication and processing will be also tackled.

Probing Access Resistance of Solid-state Nanopores with a Scanning Probe Microscope Tip

An apparatus that integrates solid-state nanopore ionic current measurement with a Scanning Probe Microscope has been developed. When a micrometer-scale scanning probe tip is near a voltage biased nanometer-scale pore (10-100 nm), the tip partially blocks the flow of ions to the pore and increases the pore access resistance. The apparatus records the current blockage caused by the probe tip and the location of the tip simultaneously. By measuring the current blockage map near a nanopore as a function of the tip position in 3D space in salt solution, we estimate the relative pore resistance increase due to the tip, ΔR/R(0), as a function of the tip location, nanopore geometry, and salt concentration. The amplitude of ΔR/R(0) also depends on the ratio of the pore length to its radius as Ohm's law predicts. When the tip is very close to the pore surface, ~10 nm, our experiments show that ΔR/R(0) depends on salt concentration as predicted by the Poisson and Nernst-Planck equations. Furthermore, our measurements show that ΔR/R(0) goes to zero when the tip is about five times the pore diameter away from the center of the pore entrance. The results in this work not only demonstrate a way to probe the access resistance of nanopores experimentally, they also provide a way to locate the nanopore in salt solution, and open the door to future nanopore experiments for detecting single biomolecules attached to a probe tip.

Stacked graphene-Al2O3 nanopore sensors for sensitive detection of DNA and DNA-protein complexes

We report the development of a multilayered graphene-Al(2)O(3) nanopore platform for the sensitive detection of DNA and DNA-protein complexes. Graphene-Al(2)O(3) nanolaminate membranes are formed by sequentially depositing layers of graphene and Al(2)O(3), with nanopores being formed in these membranes using an electron-beam sculpting process. The resulting nanopores are highly robust, exhibit low electrical noise (significantly lower than nanopores in pure graphene), are highly sensitive to electrolyte pH at low KCl concentrations (attributed to the high buffer capacity of Al(2)O(3)), and permit the electrical biasing of the embedded graphene electrode, thereby allowing for three terminal nanopore measurements. In proof-of-principle biomolecule sensing experiments, the folded and unfolded transport of single DNA molecules and RecA-coated DNA complexes could be discerned with high temporal resolution. The process described here also enables nanopore integration with new graphene-based structures, including nanoribbons and nanogaps, for single-molecule DNA sequencing and medical diagnostic applications.

DNA sequencing by nanopore-induced photon emission

Nanopore-based DNA analysis is an extremely attractive area of research due to the simplicity of the method, and the ability to not only probe individual molecules, but also to detect very small amounts of genomic material. Here, we describe the materials and methods of a novel, nanopore-based, single-molecule DNA sequencing system that utilizes optical detection. We convert target DNA according to a binary code, which is recognized by molecular beacons with two types of fluorophores. Solid-state nanopores are then used to sequentially strip off the beacons, leading to a series of photon bursts that can be detected with a custom-made microscope. We do not use any enzymes in the readout stage; thus, our system is not limited by the highly variable processivity, lifetime, and inaccuracy of individual enzymes that can hinder throughput and reliability. Furthermore, because our system uses purely optical readout, we can take advantage of high-end, wide-field imaging devices to record from multiple nanopores simultaneously. This allows an extremely straightforward parallelization of our system to nanopore arrays.

Nanopore sensors for nucleic acid analysis

Nanopore analysis is an emerging technique that involves using a voltage to drive molecules through a nanoscale pore in a membrane between two electrolytes, and monitoring how the ionic current through the nanopore changes as single molecules pass through it. This approach allows charged polymers (including single-stranded DNA, double-stranded DNA and RNA) to be analysed with subnanometre resolution and without the need for labels or amplification. Recent advances suggest that nanopore-based sensors could be competitive with other third-generation DNA sequencing technologies, and may be able to rapidly and reliably sequence the human genome for under $1,000. In this article we review the use of nanopore technology in DNA sequencing, genetics and medical diagnostics.

Lipid bilayer coated Al(2)O(3) nanopore sensors: towards a hybrid biological solid-state nanopore

Solid-state nanopore sensors are highly versatile platforms for the rapid, label-free electrical detection and analysis of single molecules, applicable to next generation DNA sequencing. The versatility of this technology allows for both large scale device integration and interfacing with biological systems. Here we report on the development of a hybrid biological solid-state nanopore platform that incorporates a highly mobile lipid bilayer on a single solid-state Al(2)O(3) nanopore sensor, for the potential reconstitution of ion channels and biological nanopores. Such a system seeks to combine the superior electrical, thermal, and mechanical stability of Al(2)O(3) solid-state nanopores with the chemical specificity of biological nanopores. Bilayers on Al(2)O(3) exhibit higher diffusivity than those formed on TiO(2) and SiO(2) substrates, attributed to the presence of a thick hydration layer on Al(2)O(3), a key requirement to preserving the biological functionality of reconstituted membrane proteins. Molecular dynamics simulations demonstrate that the electrostatic repulsion between the dipole of the DOPC headgroup and the positively charged Al(2)O(3) surface may be responsible for the enhanced thickness of this hydration layer. Lipid bilayer coated Al(2)O(3) nanopore sensors exhibit excellent electrical properties and enhanced mechanical stability (GΩ seals for over 50 h), making this technology ideal for use in ion channel electrophysiology, the screening of ion channel active drugs and future integration with biological nanopores such as α-hemolysin and MspA for rapid single molecule DNA sequencing. This technology can find broad application in bio-nanotechnology.

Controlling DNA translocation through gate modulation of nanopore wall surface charges

One major challenge of nanopore-based DNA sequencing technology is to find an efficient way to reduce DNA translocation speed so that each nucleotide can reside long enough in the pore for interrogation. Here we report the electrical tuning of DNA translocation speed by gate modulation of nanopore wall surface charges. We find that native surface-charge-induced counterions in the electroosmotic layer substantially enhance advection flow of fluid, which exerts stronger dragging forces on the translocating DNA, and thereby lowering the DNA translocation speed. We propose a feedback device architecture to regulate DNA translocation by modulating the effective wall surface charge density σw*via lateral gate voltages--at the beginning, a positive gate bias is applied to weaken σw* in order to enhance the capture rate of DNA molecule; upon detection of ionic current variance indicating DNA has been driven into the nanopore, gate bias is turned to be negative so that σw* is reinforced and DNA translocation is retarded. We show that a gate electric field can dramatically decrease the DNA translocation speed at a rate about 55 μm/s per 1 mV/nm.

High-k dielectric Al₂O₃ nanowire and nanoplate field effect sensors for improved pH sensing

Over the last decade, field-effect transistors (FETs) with nanoscale dimensions have emerged as possible label-free biological and chemical sensors capable of highly sensitive detection of various entities and processes. While significant progress has been made towards improving their sensitivity, much is yet to be explored in the study of various critical parameters, such as the choice of a sensing dielectric, the choice of applied front and back gate biases, the design of the device dimensions, and many others. In this work, we present a process to fabricate nanowire and nanoplate FETs with Al(2)O(3) gate dielectrics and we compare these devices with FETs with SiO(2) gate dielectrics. The use of a high-k dielectric such as Al(2)O(3) allows for the physical thickness of the gate dielectric to be thicker without losing sensitivity to charge, which then reduces leakage currents and results in devices that are highly robust in fluid. This optimized process results in devices stable for up to 8 h in fluidic environments. Using pH sensing as a benchmark, we show the importance of optimizing the device bias, particularly the back gate bias which modulates the effective channel thickness. We also demonstrate that devices with Al(2)O(3) gate dielectrics exhibit superior sensitivity to pH when compared to devices with SiO(2) gate dielectrics. Finally, we show that when the effective electrical silicon channel thickness is on the order of the Debye length, device response to pH is virtually independent of device width. These silicon FET sensors could become integral components of future silicon based Lab on Chip systems.

Pulsed plasma polymerization for controlling shrinkage and surface composition of nanopores

Solid-state nanopores have emerged as sensors for single molecules and these have been employed to examine the biophysical properties of an increasingly large variety of biomolecules. Herein we describe a novel and facile approach to precisely adjust the pore size, while simultaneously controlling the surface chemical composition of the solid-state nanopores. Specifically, nanopores fabricated using standard ion beam technology are shrunk to the requisite molecular dimensions via the deposition of highly conformal pulsed plasma generated thin polymeric films. The plasma treatment process provides accurate control of the pore size as the conformal film deposition depends linearly on the deposition time. Simultaneously, the pore and channel chemical compositions are controlled by appropriate selection of the gaseous monomer and plasma conditions employed in the deposition of the polymer films. The controlled pore shrinkage is characterized with high resolution AFM, and the film chemistry of the plasma generated polymers is analyzed with FTIR and XPS. The stability and practical utility of this new approach is demonstrated by successful single molecule sensing of double-stranded DNA. The process offers a viable new advance in the fabrication of tailored nanopores, in terms of both the pore size and surface composition, for usage in a wide range of emerging applications.

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.

Biotechnical and other applications of nanoporous membranes

Recent advances mean that arrays of nearly uniform cylindrical, conical and pyramidal shaped pores can be produced in several types of substrates. Surface modification of nanopore surfaces can give unique mass transport characteristics that have recently been explored for biomolecule separation, detection and purification. Recent interest has focused on the use of nanoporous membranes for mass transfer diodes that act analogous to solid-state devices based on electron conduction. Asymmetric pores such as conical pores can show superior performance characteristics compared to traditional cylindrical pores in ion rectification. However, many phenomena for membranes with asymmetric pores still remain to be exploited in biomolecular separation, biosensing, microfluidics, logic gates, and energy harvesting and storage.

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.

Porous graphene as an atmospheric nanofilter

The fabrication of nanoscale membranes exhibiting high selectivity is an emerging field of research. The possibility to use bottom-up approaches to fabricate a filter with porous graphene and analyze its functionality with first principle calculations is investigated. Here, the porous network is produced by self-assembly of the hexaiodo-substituted macrocycle cyclohexa-m-phenylene (CHP). The resulting porous network exhibits an extremely high selectivity in favor of H(2) and He among other atmospheric gases, such as Ne, O(2), N(2), CO, CO(2), NH(3), and Ar. The presented membrane is superior to traditional filters using polymers or silica and could have great potential for further technological applications such as gas sensors or fuel cells.

Detection of nucleic acids with graphene nanopores: ab initio characterization of a novel sequencing device

We report an ab initio density functional theory study of the interaction of four nucleobases, cytosine, thymine, adenine, and guanine, with a novel graphene nanopore device for detecting the base sequence of a single-stranded nucleic acid (ssDNA or RNA). The nucleobases were inserted into a pore in a graphene nanoribbon, and the electrical current and conductance spectra were calculated as functions of voltage applied across the nanoribbon. The conductance spectra and charge densities were analyzed in the presence of each nucleobase in the graphene nanopore. The results indicate that due to significant differences in the conductance spectra the proposed device has adequate sensitivity to discriminate between different nucleotides. Moreover, we show that the nucleotide conductance spectrum is affected little by its orientation inside the graphene nanopore. The proposed technique may be extremely useful for real applications in developing ultrafast, low-cost DNA sequencing methods.

Computational microscopy of the role of protonable surface residues in nanoprecipitation oscillations

A novel phenomenon has recently been reported in polymeric nanopores. This phenomenon, so-called nanoprecipitation, is characterized by the transient formation of precipitates in the nanopore lumen, producing a sequence of low and high conductance states in the ionic current through the pore. By means of all-atom molecular dynamics simulations, we studied nanoprecipitation for polyethylene terephthalate nanopore immersed in electrolytic solution containing calcium phosphate, covering a total simulation time of 1.24 micros. Our results suggest that protonable surface residues at the nanopore surface, namely carboxyl groups, trigger the formation of precipitates that strongly adhere to the surface, blocking the pore and producing the low conductance state. On the basis of the simulations, we propose a mechanism for the formation of the high conductance state; the mechanism involves detachment of the precipitate from the surface due to reprotonation of carboxyl groups and subsequent translocation of the precipitate out of the pore.

DNA translocation through graphene nanopores

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

Fabrication of metallized nanopores in silicon nitride membranes for single-molecule sensing

The fabrication and characterization of a metallized nanopore structure for the sensing of single molecules is described. Pores of varying diameters (>10 nm) are patterned into free-standing silicon nitride membranes by electron-beam lithography and reactive ion etching. Structural characterization by transmission electron microscopy (TEM) and tomography reveals a conical pore shape with a 40 degrees aperture. Metal films of Ti/Au are vapor deposited and the pore shape and shrinking are studied as a function of evaporated film thickness. TEM tomography analysis confirms metalization of the inner pore walls as well as conservation of the conical pore shape. In electrical measurements of the transpore current in aqueous electrolyte solution, the pores feature very low noise. The applicability of the metallized pores for stochastic sensing is demonstrated in real-time translocation experiments of single lambda-DNA molecules. We observe exceptionally long-lasting current blockades with a fine structure of distinct current levels, suggesting an attractive interaction between the DNA and the PEGylated metallic pore walls.

Molecular diagnostics for personal medicine using a nanopore

Semiconductor nanotechnology has created the ultimate analytical tool: a nanopore with single molecule sensitivity. This tool offers the intriguing possibility of high-throughput, low cost sequencing of DNA with the absolute minimum of material and preprocessing. The exquisite single molecule sensitivity obviates the need for costly and error-prone procedures like polymerase chain reaction amplification. Instead, nanopore sequencing relies on the electric signal that develops when a DNA molecule translocates through a pore in a membrane. If each base pair has a characteristic electrical signature, then ostensibly a pore could be used to analyze the sequence by reporting all of the signatures in a single read without resorting to multiple DNA copies. The potential for a long read length combined with high translocation velocity should make resequencing inexpensive and allow for haplotyping and methylation profiling in a chromosome.

DNA Sensing using Nano-crystalline Surface Enhanced Al(2)O(3) Nanopore Sensors

A new solid-state, Al(2)O(3) nanopore sensor with enhanced surface properties for the real-time detection and analysis of individual DNA molecules is reported. Nanopore formation using electron beam based decomposition transformed the local nanostructure and morphology of the pore from an amorphous, stoichiometric structure (O to Al ratio of 1.5) to a hetero-phase crystalline network, deficient in O (O to Al ratio of ~0.6). Direct metallization of the pore region was observed during irradiation, thereby permitting the potential fabrication of nano-scale metallic contacts in the pore region with potential application to nanopore-based DNA sequencing. Dose dependent phase transformations to purely γ and/or α-phase nanocrystallites were also observed during pore formation allowing for surface charge engineering at the nanopore/fluid interface. DNA transport studies revealed an order of magnitude reduction in translocation velocities relative to alternate solid-state architectures, accredited to high surface charge density and the nucleation of charged nanocrystalline domains. The unique surface properties of Al(2)O(3) nanopore sensors makes them ideal for the detection and analysis of ssDNA, dsDNA, RNA secondary structures and small proteins. These nano-scale sensors may also serve as a useful tool in studying the mechanisms driving biological processes including DNA-protein interactions and enzyme activity at the single molecule level.

The enhanced alcohol-sensing response of ultrathin WO3 nanoplates

Chemical sensors based on semiconducting metal oxide nanocrystals are of academic and practical significance in industrial processing and environment-related applications. Novel alcohol response sensors using two-dimensional WO(3) nanoplates as active elements have been investigated in this paper. Single-crystalline WO(3) nanoplates were synthesized through a topochemical approach on the basis of intercalation chemistry (Chen et al 2008 Small 4 1813). The as-obtained WO(3) nanoplate pastes were coated on the surface of an Al(2)O(3) ceramic microtube with four Pt electrodes to measure their alcohol-sensing properties. The results show that the WO(3) nanoplate sensors are highly sensitive to alcohols (e.g., methanol, ethanol, isopropanol and butanol) at moderate operating temperatures (260-360 degrees C). For butanol, the WO(3) nanoplate sensors have a sensitivity of 31 at 2 ppm and 161 at 100 ppm, operating at 300 degrees C. For other alcohols, WO(3) nanoplate sensors also show high sensitivities: 33 for methanol at 300 ppm, 70 for ethanol at 200 ppm, and 75 for isopropanol at 200 ppm. The response and recovery times of the WO(3) nanoplate sensors are less than 15 s for all the test alcohols. A good linear relationship between the sensitivity and alcohol concentrations has been observed in the range of 2-300 ppm, whereas the WO(3) nanoparticle sensors have not shown such a linear relationship. The sensitivities of the WO(3) nanoplate sensors decrease and their response times become short when the operating temperatures increase. The enhanced alcohol-sensing performance could be attributed to the ultrathin platelike morphology, the high crystallinity and the loosely assembling structure of the WO(3) nanoplates, due to the advantages of the effective adsorption and rapid diffusion of the alcohol molecules.

Perspectives and challenges of emerging single-molecule DNA sequencing technologies

The growing demand for analysis of the genomes of many species and cancers, for understanding the role of genetic variation among individuals in disease, and with the ultimate goal of deciphering individual human genomes has led to the development of non-Sanger reaction-based technologies towards rapid and inexpensive DNA sequencing. Recent advancements in new DNA sequencing technologies are changing the scientific horizon by dramatically accelerating biological and biomedical research and promising an era of personalized medicine for improved human health. Two single-molecule sequencing technologies based on fluorescence detection are already in a working state. The newly launched and emerging single-molecule DNA sequencing approaches are reviewed here. The current challenges of these technologies and potential methods of overcoming these challenges are critically discussed. Further research and development of single-molecule sequencing will allow researchers to gather nearly error-free genomic data in a timely and inexpensive manner.