Resistive-pulse DNA detection with a conical nanopore sensor.

In this paper, we describe resistive-pulse sensing of two large DNAs, a single-stranded phage DNA (7250 bases) and a double-stranded plasmid DNA (6600 base pairs), using a conically shaped nanopore in a track-etched polycarbonate membrane as the sensing element. The conically shaped nanopore had a small-diameter (tip) opening of 40 nm and a large-diameter (base) opening of 1.5 microm. The DNAs were detected using the resistive-pulse, sometimes called stochastic sensing, method. This entails applying a transmembrane potential difference and monitoring the resulting ion current flowing through the nanopore. The phage DNA was driven electrophoretically through the nanopore (from tip to base), and these translocation events were observed as transient blocks in the ion current. We found that the frequency of these current-block events scales linearly with the concentration of the DNA and with the magnitude of the applied transmembrane potential. Increasing the applied transmembrane potential also led to a decrease in the duration of the current-block events. We also analyzed current-block events for the double-stranded plasmid DNA. However, because this DNA is too large to enter the tip opening of the nanopore, it could not translocate the pore. As a result, much shorter duration current-block events were observed, which we postulate are associated with bumping of the double-stranded DNA against the tip opening.

DNA-nanotube artificial ion channels.

There is considerable interest in developing chemical devices that mimic the function of biological ion channels. We recently described such a device, which consisted of a single conically shaped gold nanotube embedded within a polymeric membrane. This device mimicked one of the key functions of voltage-gated ion channels: the ability to strongly rectify the ionic current flowing through it. The data obtained were interpreted using a simple electrostatic model. While the details are still being debated, it is clear that ion-current-rectification in biological ion channels is more complicated and involves physical movement of an ionically charged portion of the channel in response to a change in the transmembrane potential. We report here artificial ion channels that rectify the ion current flowing through them via this "electromechanical" mechanism. These artificial channels are also based on conical gold nanotubes, but with the critical electromechanical response provided by single-stranded DNA molecules attached to the nanotube walls.

Electrophoretic capture and detection of nanoparticles at the opening of a membrane pore using scanning electrochemical microscopy.

Stochastic electrophoretic capture of individual nanometer-scale particles at the small opening of a conically shaped nanopore in a synthetic membrane is described. Particle capture is sensed using a scanning electrochemical microscope (SECM) to measure the decrease in the transport rate of a redox-active molecule through the pore. The SECM tip is positioned at the larger backside opening of pore and used to amperometrically monitor the transport rate prior, during, and after particle capture. Following capture, the particle is released by electrophoretically driving it out of the pore opening and back into the solution. The capture and release method is demonstrated by detection of charged polystyrene spheres (43-150-nm diameter) using a polycarbonate membrane with conically shaped pores, the small opening of the pore having a diameter of 60 nm. The inverse of the time to capture polystyrene spheres increases with particle concentration over the range 10(8)-10(10) particles/mL. Selective detection based on nanoparticle charge and size is also demonstrated. A quantitative theoretical description of the rate of particle capture is presented, and the physical mechanism of particle capture, based on the balance of electrostatic and entropic forces, is considered.

Conical-nanotube ion-current rectifiers: the role of surface charge.

Ion channels are protein pores that span cell membranes and open and close in response to stimuli like changes in the transmembrane potential, binding of a ligand, or mechanical stress. When open, ions pass through the pore, and hence across the cell membrane, and when closed, ion-transport is precluded. Hence, these channels are nanodevices that have a current-rectification function. There is intense research effort aimed at understanding the molecular-level mechanism for this function. One approach for elucidating the mechanism is to construct a simple abiotic system that mimics this function and to use the mechanistic details of this mimic as a guide to understand the more complex biological channel. We describe here such an abiotic mimic: a synthetic membrane that contains a single conical gold nanotube. The advantage of this mimic is that the surface charge and chemistry of the nanotube wall can be varied, at will, by judicious choice of electrolyte or by thiol chemisorption. This has allowed us to make conical Au nanotubes that rectify the ion current and, just as importantly, to definitively elucidate the mechanism of this function.

DNA-functionalized nanotube membranes with single-base mismatch selectivity.

We describe synthetic membranes in which the molecular recognition chemistry used to accomplish selective permeation is DNA hybridization. These membranes contain template-synthesized gold nanotubes with inside diameters of 12 nanometers, and a "transporter" DNA-hairpin molecule is attached to the inside walls of these nanotubes. These DNA-functionalized nanotube membranes selectively recognize and transport the DNA strand that is complementary to the transporter strand, relative to DNA strands that are not complementary to the transporter. Under optimal conditions, single-base mismatch transport selectivity can be obtained.

Layer-by-layer nanotube template synthesis.

Electroless deposition of gold on the pore walls of polycarbonate templates is currently the best known method for controlling inside diameters of template-synthesized nanotubes. It would be very useful to have alternative template-based synthetic chemistries that yield nanotubes composed of other materials, but which still allow for precise control over the nanotube wall thickness and i.d. A film-formation process that is based on layer-by-layer deposition of the film-forming material along the pore walls of the template membrane provides this desired alternative synthetic chemistry. We describe here the use of Mallouk's alpha,omega-diorganophosphonate/Zr layer-by-layer film-forming method for preparing nanotubes within the pores of alumina template membranes. We have found that this method allows accurate, quantitative, and predictable control over the wall thickness, and thus i.d., of the layered nanotubes obtained.

Conical nanopore membranes. Preparation and transport properties.

We have been investigating applications of nanopore membranes in analytical chemistry-specifically in membrane-based bioseparations, in electroanalytical chemistry, and in the development of new approaches to biosensor design. Membranes that have conically shaped pores (as opposed to the more conventional cylindrical shape) may offer some advantages for these applications. We describe here a simple plasma-etch method that converts cylindrical nanopores in track-etched polymeric membranes into conically shaped pores. This method allows for control of the shape of the resulting conical nanopores. For example, the plasma-etched pores may be cylindrical through most of the membrane thickness blossoming into cones at one face of the membrane (trumpet-shaped), or they may be nearly perfect cones. The key advantage of the conical pore shape is a dramatic enhancement in the rate of transport through the membrane, relative to an analogous cylindrical pore membrane. We demonstrate this here by measuring the ionic resistances of the plasma-etched conical pore membranes.

Synthetic single-nanopore and nanotube membranes.

There is increasing interest in investigating transport and electrochemical phenomena in synthetic membrane samples that contain a single pore of nanoscopic diameter. Approaches used to date for preparing such single-nanopore membranes include microfabrication-based methods, the track-etch method, and a method based on the incorporation of a single fullerene nanotube within a synthetic membrane. We describe here an alternative approach that we believe is easier and more accessible than the previously described methods. This method is based on a very low pore density track-etch membrane obtained from commercial sources. Fluorescence microscopy is used to identify and isolate a single nanopore in this membrane. Membrane samples containing single nanopores with diameters as small as 30 nm have been prepared. Furthermore, we show here that an electroless plating method can be used to deposit a gold nanotube within the single nanopore, and this provides a route for further decreasing the inside diameter of the pore. A single-nanotube membrane with an electrochemically determined inside diameter of approximately 2 nm was prepared and evaluated.