Nanopore Fabrication by Controlled Dielectric Breakdown

Nanofabrication techniques for achieving dimensional control at the nanometer scale are generally equipment-intensive and time-consuming. The use of energetic beams of electrons or ions has placed the fabrication of nanopores in thin solid-state membranes within reach of some academic laboratories, yet these tools are not accessible to many researchers and are poorly suited for mass-production. Here we describe a fast and simple approach for fabricating a single nanopore down to 2-nm in size with sub-nm precision, directly in solution, by controlling dielectric breakdown at the nanoscale. The method relies on applying a voltage across an insulating membrane to generate a high electric field, while monitoring the induced leakage current. We show that nanopores fabricated by this method produce clear electrical signals from translocating DNA molecules. Considering the tremendous reduction in complexity and cost, we envision this fabrication strategy would not only benefit researchers from the physical and life sciences interested in gaining reliable access to solid-state nanopores, but may provide a path towards manufacturing of nanopore-based biotechnologies.Comment: 19 pages, 4 figures. Supplementary information contains 22 pages, 11 figures and 2 tables - A version of this manuscript was first submitted for publication on April 23rd, 2013. It is currently under review at another journa

Descreening of Field Effect in Electrically Gated Nanopores

This modeling work investigates the electrical modulation characteristics of field-effect gated nanopores. Highly nonlinear current modulations are observed in nanopores with non-overlapping electric double layers, including those with pore diameters 100 times the Debye screening length. We attribute this extended field-effect gating to a descreening effect, i.e. the counter-ions do not fully relax to screen the gating potential due to the presence of strong ionic transport

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

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94472/1/elps4443.pd

Nanopore surface coating delivers nanopore size and shape through conductance-based sizing

The performance of nanopore single-molecule sensing elements depends intimately on their physical dimensions and surface chemical properties. These factors underpin the dependence of the nanopore ionic conductance on electrolyte concentration, yet the measured, or modeled, dependence only partially illuminates the details of geometry and surface chemistry. Using the electrolyte-dependent conductance data before and after selective surface functionalization of solid-state nanopores, however, introduces more degrees of freedom and improves the performance of conductance-based nanopore characterizations. Sets of representative nanopore profiles were used to generate conductance data, and the nanopore shape and exact dimensions were identified, through conductance alone, by orders-of-magnitude 3 reductions in the geometry optimization metrics. The optimization framework could similarly be used to evaluate the nanopore surface coating thickness

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 ~$1,000 in ~24 h.Molecular and Cellular BiologyPhysic

Fabrication of a single sub-micron pore spanning a single crystal (100) diamond membrane and impact on particle translocation

The fabrication of sub-micron pores in single crystal diamond membranes, which span the entirety of the membrane, is described for the first time, and the translocation properties of polymeric particles through the pore investigated. The pores are produced using a combination of laser micromachining to form the membrane and electron beam induced etching to form the pore. Single crystal diamond as the membrane material, has the advantages of chemical stability and durability, does not hydrate and swell, has outstanding electrical properties that facilitate fast, low noise current-time measurements and is optically transparent for combined optical-conductance sensing. The resulting pores are characterized individually using both conductance measurements, employing a microcapillary electrochemical setup, and electron microscopy. Proof-of-concept experiments to sense charged polystyrene particles as they are electrophoretically driven through a single diamond pore are performed, and the impact of this new pore material on particle translocation is explored. These findings reveal the potential of diamond as a platform for pore-based sensing technologies and pave the way for the fabrication of single nanopores which span the entirety of a diamond membrane

Microcantilever actuation generated by redox-induced surface stress

Electrochemically-induced changes in surface stress at the solid-liquid interface are measured using a differential cantilever-based sensor. The simultaneous, in situ measurements of the current (charge) and interfacial stress changes are performed by employing an AFM cantilever as both the working electrode (in a conventional three-probe electrochemical cell configuration) and as the mechanical transducer (bending of the cantilever). The custom-built instrument achieves a surface stress sensitivity of 1x10-4 N/m and a dynamic range of 5x105. Combining electrochemistry with cantilever-based sensing provides the extra surface characterization capability essential for the interpretation of the origin of the surface stress.The objective of the present study is to gain a better understanding of the mechanisms responsible for the nanomechanical motion of cantilever sensors during adsorption and absorption processes. The study of these simple model systems will lead to a general understanding of the cantilever-based sensor's response and provide insights into the physical origin of the measured surface stress.The surface stress generated by the electrochemically-controlled absorption of ions into a thin polypyrrole film is investigated. A compressive change in surface stress of about -2 N/m is measured when the polymer is electrochemically switched between its oxidized and neutral (swollen) state. The volume change of the polymer phase with respect to the gold-coated cantilever is shown to be responsible for the mechanical motion observed.The potential-induced surface stress and surface energy change on an Au(111)-textured cantilever, in a 0.1 M HClO4 electrolyte, are simultaneously measured. These measurements revealed that for solid electrodes these two thermodynamic parameters are significantly different. In the double layer region, a surface stress change of -0.55 +/-0.06 N/m is measured during ClO4- adsorption whereas the surface energy variation is smaller by one order of magnitude. The origin of the surface stress change at the metal-electrolyte interface is understood by the variation in electron density at the surface which alters the inter-atomic bonds strength between surface atoms, while the specificity of adsorption of ions is found to be mostly responsible for the fine structure of the surface stress profile

Analysis of nanopore data: classification strategies for an unbiased curation of single-molecule events from DNA nanostructures

Nanopores are versatile single-molecule sensors that are being used to sense increasingly complex mixtures of structured molecules, with applications in molecular data storage and disease biomarker detection. However, increased molecular complexity presents additional challenges to the analysis of nanopore data including more translocation events being rejected for not matching an expected signal structure and a greater risk of selection bias entering this event curation process. To highlight these challenges, here we present the analysis of a model molecular system consisting of a nanostructured DNA molecule attached to a linear DNA carrier. We make use of recent advances in the event segmentation capabilities of Nanolyzer, a graphical analysis tool provided for nanopore event fitting, and describe approaches to event substructure analysis. In the process, we identify and discuss important sources of selection bias in that emerge in the analysis of this molecular system and consider the complicating effects of molecular conformation and variable experimental conditions (e.g. pore diameter). We then present additional refinements to existing analysis techniques, allowing for improved separation of multiplexed samples, fewer translocation events rejected as false negatives, and a wider range of experimental conditions for which accurate molecular information can be extracted. Increasing the coverage of analyzed events within nanopore data is not only important for characterizing complex molecular samples with high fidelity, but is also becoming essential to the generation of accurate, unbiased training data as machine learning approaches to data analysis and event identification continue to increase in prevalence