Ken Healy

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.

Nanopore-based single-molecule DNA analysis

Nanopore-based DNA analysis is a single-molecule technique with revolutionary potential. It promises to carry out a range of analyses, orders of magnitude faster than current methods, including length measurement, specific sequence detection, single-molecule dynamics and even de novo sequencing. The concept involves using an applied voltage to drive DNA molecules through a narrow pore that separates chambers of electrolyte solution. This voltage also drives a flow of electrolyte ions through the pore, measured as an electric current. When molecules pass through the pore, they block the flow of ions and, thus, their structure and length can be determined based on the degree and duration of the resulting current reductions. In this review, I explain the nanopore-based DNA analysis concept and briefly explore its historical foundations, before discussing and summarizing all experimental results reported to date. I conclude with a summary of the obstacles that must be overcome for it to realize its promised potential.

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.

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.

Polystyrene Particles Reveal Pore Substructure As They Translocate

In this article, we report resistive-pulse sensing experiments with cylindrical track-etched PET pores, which reveal that the diameters of these pores fluctuate along their length. The resistive pulses generated by polymer spheres passing through these pores have a repeatable pattern of large variations corresponding to these diameter changes. We show that this pattern of variations enables the unambiguous resolution of multiple particles simultaneously in the pore, that it can detect transient sticking of particles within the pore, and that it can confirm whether any individual particle completely translocates the pore. We demonstrate that nonionic surfactant has a significant impact on particle velocity, with the velocity decreasing by an order of magnitude for a similar increase in surfactant concentration. We also show that these pores can differentiate by particle size and charge, and we explore the influence of electrophoresis, electroosmosis, and pore size on particle motion. These results have practical importance for increasing the speed of resistive-pulse sensing, optimizing the detection of specific analytes, and identifying particle shapes.

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

We report on the fabrication, simulation, and characterization of insulated nanoelectrodes aligned with nanopores in low‐capacitance silicon nitride membrane chips. We are exploring these devices for the transverse sensing of DNA molecules as they are electrophoretically driven through the nanopore in a linear fashion. While we are currently working with relatively large nanopores (6–12 nm in diameter) to demonstrate the transverse detection of DNA, our ultimate goal is to reduce the size sufficiently to resolve individual nucleotide bases, thus sequencing DNA as it passes through the pore. We present simulations and experiments that study the impact of insulating these electrodes, which is important to localize the sensing region. We test whether the presence of nanoelectrodes or insulation affects the stability of the ionic current flowing through the nanopore, or the characteristics of DNA translocation. Finally, we summarize the common device failures and challenges encountered during fabrication and experiments, explore the causes of these failures, and make suggestions on how to overcome them in the future.

Tuning ion current rectification in asymmetric nanopores by signal mixing

Transport properties of asymmetric and rectifying single nanopores in polymer films were studied in the presence of a sum of two periodic, rectangular voltage signals, with the aim of testing signal mixing as a tool for tuning ion current rectification. Current-voltage curves and net ion currents were recorded when the two voltage signals were added with a controlled phase difference. We show that changing the ratio of frequencies, the phase difference and amplitude of the two voltage inputs gives a new possibility to enhance, hinder or cancel the rectifying properties of the nanoporous system. Our experimental results are explained by a model of a doubly rocked ratchet in the adiabatic regime, presented in Europhys. Lett., 67 (2004) 179.

Noise Properties of Ion Current in Rectifying Nanopores

Studying noise properties of ion currents in nanopores can improve detection limits for nanopore sensors as well as give insight into behavior of transport at the nanoscale. We focused on the 1/f⊥alpha noise that is observed in the low frequency regime of the ion current power spectra with the exponent alpha∼1. We found that 1/f noise in single conically shaped nanopores in polymer films and glass nanopipettes exhibits asymmetric noise properties with respect to voltage polarity which are not observed for cylindrical and silicon nitride nanopores. The noise asymmetry is shown by the normalized power spectra, which present the noise amplitude at a given frequency, typically 1 Hz for these measurements, divided by the ion current squared. The conically shaped structures rectify the ion current and the currents for the forward bias exhibit noise that increases with voltage in an exponential manner, and are weakly KCl concentration dependent. The normalized noise of currents in the reverse bias is typically voltage-independent but increases with the increase of KCl concentration. The difference in noise properties of the currents is most pronounced when the pore diameter is comparable to the thickness of the electrical double-layer. We discuss two models, which could explain the observed effects: (i) presence of air bubbles, and (ii) crowding of ions at the pore entrance.