Electrokinetic DNA transport in a nanopore membrane

Modulation of electrophoresis, electroosmosis and diffusion for electrical transport of proteins through a solid-state nanopore

Nanopore probing of molecular level transport of proteins is strongly influenced by electrolyte type, concentration, and solution pH. As a result, electrolyte chemistry and applied voltage are critical for protein transport and impact, for example, capture rate (C_R), transport mechanism (i.e., electrophoresis, electroosmosis or diffusion), and 3D conformation (e.g., chaotropic vs. kosmotropic effects). In this study, we explored these using 0.5–4 M LiCl and KCl electrolytes with holo-human serum transferrin (hSTf) protein as the model protein in both low (±50 mV) and high (±400 mV) electric field regimes. Unlike in KCl, where events were purely electrophoretic, the transport in LiCl transitioned from electrophoretic to electroosmotic with decreasing salt concentration while intermediate concentrations (i.e., 2 M and 2.5 M) were influenced by diffusion. Segregating diffusion-limited capture rate (R_diff) into electrophoretic (R_diff,EP) and electroosmotic (R_diff,EO) components provided an approach to calculate the zeta-potential of hSTf (ζ_hSTf) with the aid of C_R and zeta potential of the nanopore surface (ζ_pore) with (ζ_pore–ζ_hSTf) governing the transport mechanism. Scrutinization of the conventional excluded volume model revealed its shortcomings in capturing surface contributions and a new model was then developed to fit the translocation characteristics of proteins.

Figure shows hSTf protein translocating through a solid-state nanopore under an applied electric field and the resulting current traces. The transport mechanism is determined by the interplay of electrophoretic and electroosmotic force.

Transport properties of track-etched membranes having variable effective pore-lengths

The transport rate of molecules through polymeric membranes is normally limited because of their micrometer-scale thickness which restricts their suitability for more practical application. To study the effect of effective pore length on the transport behavior, polymer membranes containing cylindrical and asymmetric-shaped nanopores were prepared through a two-step ion track-etching technique. Permeation experiments were performed separately to investigate the transport properties (molecular flux and selectivity) of these track-etched membranes. The permeation data shows that the molecular flux across membranes containing asymmetric nanopores is higher compared to those having cylindrical pores. On the other hand, the cylindrical pore membranes exhibit higher selectivity than asymmetric pores for the permeation of charged molecules across the membrane. Current-voltage (I-V) measurements of single-pore membranes further verify that asymmetric pores exhibit lower resistance for the flow of ions and therefore show higher currents than cylindrical pores. Moreover, unmodified and polyethyleneimine (PEI) modified asymmetric-shaped pore membranes were successfully used for the separation of cationic and anionic analyte molecules from their mixture, respectively. In this study, two distinct effects (pore geometry and pore density, i.e. number of pores cm(-2)), which mainly influence membrane selectivity and molecular transport rates, were thoroughly investigated in order to optimize the membrane performance. In this context, we believe that membranes with high molecular transport rates could readily find their application in molecular separation and controlled drug delivery processes.

Resistive pulse sensing of magnetic beads and supraparticle structures using tunable pores

Tunable pores (TPs) have been used for resistive pulse sensing of 1 μm superparamagnetic beads, both dispersed and within a magnetic field. Upon application of this field, magnetic supraparticle structures (SPSs) were observed. Onset of aggregation was most effectively indicated by an increase in the mean event magnitude, with data collected using an automated thresholding method. Simulations enabled discrimination between resistive pulses caused by dimers and individual particles. Distinct but time-correlated peaks were often observed, suggesting that SPSs became separated in pressure-driven flow focused at the pore constriction. The distinct properties of magnetophoretic and pressure-driven transport mechanisms can explain variations in the event rate when particles move through an asymmetric pore in either direction, with or without a magnetic field applied. Use of TPs for resistive pulse sensing holds potential for efficient, versatile analysis and measurement of nano- and microparticles, while magnetic beads and particle aggregation play important roles in many prospective biosensing applications.

Size selective DNA transport through a nanoporous membrane in a PDMS microfluidic device

A microfluidic counter current dialysis device for size based purification of DNA is described. The device consists of two polydimethylsiloxane (PDMS) channels separated by a track etched polycarbonate membrane with a 50 nm pore size. Recovery of fluorescein across the membrane was compared with 10 and 80 nucleotide (nt) ssDNA to characterize the device. Recovery of all three analytes improved with decreasing flow rate. Size selectivity was observed. Greater than 2-fold selectivity between 10 nt and 80 nt ssDNA was observed at linear velocities less than 3mm s(-1). Increasing the ionic strength of the buffer increased transport across the membrane. Recovery of 80 nt ssDNA increased over 4-fold by adding 30 mM NaCl to the buffer. The effect was size dependent as 10 nt showed a smaller increase while the recovery of fluorescein was largely unaffected by increasing the ionic strength of the buffer.

Microfluidic devices for bioapplications

Harnessing the ability to precisely and reproducibly actuate fluids and manipulate bioparticles such as DNA, cells, and molecules at the microscale, microfluidics is a powerful tool that is currently revolutionizing chemical and biological analysis by replicating laboratory bench-top technology on a miniature chip-scale device, thus allowing assays to be carried out at a fraction of the time and cost while affording portability and field-use capability. Emerging from a decade of research and development in microfluidic technology are a wide range of promising laboratory and consumer biotechnological applications from microscale genetic and proteomic analysis kits, cell culture and manipulation platforms, biosensors, and pathogen detection systems to point-of-care diagnostic devices, high-throughput combinatorial drug screening platforms, schemes for targeted drug delivery and advanced therapeutics, and novel biomaterials synthesis for tissue engineering. The developments associated with these technological advances along with their respective applications to date are reviewed from a broad perspective and possible future directions that could arise from the current state of the art are discussed.

Nanoscale control and manipulation of molecular transport in chemical analysis

The ability to understand and control molecular transport is critical to numerous chemical measurement strategies, especially as they apply to mass-limited samples in nanometer-scale structures. The characteristics of nanoscale structures and devices highlighted in the examples discussed in this article include enhanced mass transport, accessing novel physical behavior, large surface-to-volume ratio, diminished background signals, and the fact that molecular characteristics can dominate the behavior of the structure. The control of nanoscale transport is physically embodied in different structures and experiments. Those structures and experiments highlighted here are featured because of their centrality (nanochannels and nanopores), their connection to more familiar macroscale phenomena (nanoelectrodes), and/or their ability to introduce control (stimulus-responsive materials) or because they represent especially interesting possibilities (stochastic sensing structures).

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.

Reversible mechanical actuation of elastomeric nanopores

Mechanical resizing of individual nanopores in a thermoplastic polyurethane elastomer has been characterized. Specimen nanopores were conical, with smaller hole dimensions of the order of tens to hundreds of nanometres. Electrophoretic current measurements show that the estimated nanopore radius can be reversibly actuated over an order of magnitude by stretching and relaxing the elastomer. Within a working range of stretching, current is proportional to specimen extension to the power of a constant, n, which ranges from 0.9 to 2.3 for different specimens. The data indicate that scaling of the effective pore radius is super-affine. At strains below the working range, the pore size is relatively unresponsive to stretching. Macroscopic elastomer extension has been related to local radial strain (50-250 µm from the pore) using optical microscopy. Scanning electron microscopy and atomic force microscopy have been used to observe membrane surface features.

Electrokinetics induced asymmetric transport in polymeric nanonozzles

The asymmetric geometry of polymeric nanonozzles provides two different transport directions: a converging direction (from the large opening to the small opening) and a diverging direction (from the small opening to the large opening). Asymmetric transport was observed in such nanochannels for both rigid polystyrene nanoparticles and flexible DNA molecules under a DC electric bias. Small, hard nanoparticles migrate easily in the diverging direction and tend to pack inside the nanochannel in the converging direction. In contrast, large, flexible DNA molecules transport better in the converging direction than in the diverging direction. A high electric field and a high velocity gradient along the tapered region produce different geometric constrictions and vortex-like particle motions for rigid nanoparticles, and also generate various coil-stretching dynamics for DNA molecules. Such nanonozzle arrays are useful in high flux and high sieving efficiency devices for biomolecule delivery or separation, and for loading trace amounts of drugs or genes for controlled drug and gene delivery.

Fabrication of an open Au/nanoporous film by water-in-oil emulsion-induced block copolymer micelles

Water-in-oil (W/O) emulsion-induced micelles with narrow size distributions of approximately 140 nm were prepared by sonicating the polystyrene-b-poly(2-vinylpyridine) (PS-b-P2VP) block copolymer in the toluene/water (50:1 vol %). The ordered nanoporous block copolymer films with the hydrophilic P2VP interior and the PS matrix were distinctly fabricated by casting the resultant solution on substrates, followed by evaporating the organic solvent and water. The porous diameter was estimated to be about 70 nm. Here, we successfully prepared the open nanoporous nanocomposites, the P2VP domain decorated by Au (5+/-0.4 nm) nanoparticles based on the methodology mentioned. We anticipate that this novelty enhances the specific function of nanoporous films.

Nanochannel Array Plastics with Tailored Surface Chemistry

The utilization of nanoporous substrates in applications such as selective ion transport, biomolecule separation, seeded templating, and catalysis necessitates the ability to efficiently control pore surface properties. We approached this task by preparing nanoporous polymer monoliths from ABC triblock copolymer precursors that assemble into a cylindrical morphology, where the A block constitutes matrix, C is the removable minor component, and B provides the functionality on the surface of the pores. Polystyrene-polydimethylacrylamide-polylactide (PS-PDMA-PLA) triblock copolymers were prepared by a combination of controlled ring-opening and free-radical polymerization techniques. After selective etching of the PLA cylinders from shear-aligned monoliths, a nanoporous polystyrene matrix containing a hexagonally packed array of hydrophilic, PDMA-coated channels was obtained. Extremely high degrees of alignment and order could be attained, and nanoporous substrates with second-order orientation factors of as high as 0.96 were prepared. PDMA brushes inside the pores were then hydrolyzed in a controlled fashion to introduce a desired number of carboxylic acid groups to the internal pore surface. Carbodiimide mediated couplings with amines were then used to confirm the accessibility of the interior acidic groups and to render materials with different functional content. This modular approach allows for the convenient preparation of functionalized nanoporous materials from a single block copolymer precursor.

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.