Protein biosensors based on biofunctionalized conical gold nanotubes

Molecular Recognition and Specific Interactions for Biosensing Applications

Molecular recognition and specific interactions are reliable and versatile routes for site-specific and well-oriented immobilization of functional biomolecules on surfaces. The control of surface properties via the molecular recognition and specific interactions at the nanoscale is a key element for the nanofabrication of biosensors with high sensitivity and specificity. This review intends to provide a comprehensive understanding of the molecular recognition- and specific interaction-mediated biosensor fabrication routes that leads to biosensors with well-ordered and controlled structures on both nanopatterned surfaces and nanomaterials. Herein self-assembly of the biomolecules via the molecular recognition and specific interactions on nanoscaled surfaces as well as nanofabrication techniques of the biomolecules for biosensor architecture are discussed. We also describe the detection of molecular recognition- and specific interaction-mediated molecular binding as well as advantages of nanoscale detection.

Synthesis and characterization of polydiacetylene films and nanotubes

We report here the synthesis and characterization of polydiacetylene (PDA) films and nanotubes using layer-by-layer (LBL) chemistry. 10,12-Docosadiyndioic acid (DCDA) monomer was self-assembled on flat surfaces and inside of nanoporous alumina templates. UV irradiation of DCDA provided polymerized-DCDA (PDCDA) films and nanotubes. We have used zirconium-carboxylate interlayer chemistry to synthesize PDCDA multilayers on flat surfaces and in nanoporous template. PDCDA multilayers were characterized using optical (UV-vis, fluorescence, ellipsometry, FTIR) spectroscopies, ionic current-voltage ( I- V) analysis, and scanning electron microscopy. Ellipsometry, FTIR, electronic absorption and emission spectroscopies showed a uniform DCDA deposition at each deposition cycle. Our optical spectroscopic analysis indicates that carboxylate-zirconium interlinking chemistry is robust. To explain the disorganization in the alkyl portion of PDCDA multilayer films, we propose carboxylate-zirconium interlinkages act as "locks" in between PDCDA layers which restrict the movement of alkyl portion in the films. Because of this locking, the induced-stresses in the polymer chains can not be efficiently relieved. Our ionic resistance data from I- V analysis correlate well with calculated resistance at smaller number of PDCDA layers but significantly deviated for thicker PDCDA nanotubes. These differences were attributed to ion-blocking because some of the PDCDA nanotubes were totally closed and the nonohmic and permselective ionic behaviors when the diameter of the pores approaches the double-layer thickness of the solution inside of the nanotubes.

Core-shell-corona au-micelle composites with a tunable smart hybrid shell

Micelles having a core of polystyrene and a mixed shell of poly(ethylene glycol) and poly(4-vinylpyridine) were formed through self-assembly of a triblock copolymer poly(ethylene glycol)- block-polystyrene- block-poly(4-vinylpyridine) in acidic water (pH 2). Reducing the HAuCl(4)-treated micelle solution leads to the formation of the Au-micelle composites with a core of polystyrene, a hybrid shell of poly(4-vinylpyridine)/Au/poly(ethylene glycol), and a corona of poly(ethylene glycol). The gold nanoparticles with controlled sizes were anchored to poly(4-vinylpyridine) to form the physically cross-linked hybrid shell. In aqueous solution, the hybrid shell is swollen and the swollen degree is sensitive to the pH condition. Under basic conditions, the channel in the hybrid shells of the composite is produced, which renders the composites a good catalytic activity. In addition, the composites also show good stability, unchanged hydrodynamic diameter, and surface plasmon absorption under different pH conditions.

Self-supporting nanopore membranes with controlled pore size and shape

Self-supporting membranes containing either isolated or organized arrays of nanosized pores have been prepared using a nonlithographic approach by coupling sol-gel processing, thin film preparation, and templating. Specifically, polystyrene latex spheres were doped into a hybrid sol prepared from tetraethoxysilane and dimethyldiethoxysilane and the resultant sol spin cast on a sacrificial support. Upon removal of the template and the sacrificial support, the self-supporting nanopore membranes were transferred to glass for characterization by atomic force microscopy and scanning electron microscopy. Through variations in the thickness of the membranes and the size of the polystyrene latex spheres, the geometry (cylinder-like to asymmetric-like) and the dimensions of the nanopores were altered. Pores with diameters that range from 35 to 2100 nm, aspect ratios (defined as the top pore diameter divided by the bottom pore diameter) from 1-4, and depths (effective film thickness) from 50 to 1500 nms have been prepared using templates that range in diameter from 100 to 3100 nm. The method described employs "wet-chemistry", is highly versatile, and is easily amenable to modification by utilizing templates of different sizes and geometries to create stable membranes with different pore geometries and sizes that can be used as platforms for nanofiltration and/or chemical sensors.

Noise and bandwidth of current recordings from submicrometer pores and nanopores

Nanopores and submicrometer pores have recently been explored for applications ranging from detection of single molecules, assemblies of nanoparticles, nucleic acids, occurrence of chemical reactions, and unfolding of proteins. Most of these applications rely on monitoring electrical current through these pores, hence the noise and signal bandwidth of these current recordings are critical for achieving accurate and sensitive measurements. In this report, we present a detailed theoretical and experimental study on the noise and signal bandwidth of current recordings from glass and polyethylene terephthalate (PET) membranes that contain a single submicrometer pore or nanopore. We examined the theoretical signal bandwidth of two different pore geometries, and we measured the signal bandwidth of the electronics used to record the ionic current. We also investigated the theoretical noise generated by the substrate material, the pore, and the electronics used to record the current. Employing a combination of theory and experimental results, we were able to predict the noise in current traces recorded from glass and PET pores with no applied voltage with an error of less than 12% in a range of signal bandwidths from 1 to 40 kHz. In approximately half of all experiments, application of a voltage did not significantly increase the noise. In the other half of experiments, however, application of a voltage resulted in an additional source of noise. For these pores, predictions of the noise were usually still accurate within 35% error at signal bandwidths of at least 10 kHz. The power spectra of this extra noise suggested a 1/f(alpha) origin with best fits to the power spectrum for alpha = 0.4-0.8. This work provides the theoretical background and experimental data for understanding the bandwidth requirements and the main sources of noise in current recordings; it will be useful for minimizing noise and achieving accurate recordings.

Rectification in synthetic conical nanopores: a one-dimensional Poisson-Nernst-Planck model

Ion transport in biological and synthetic nanochannels is characterized by phenomena such as ion current fluctuations and rectification. Recently, it has been demonstrated that nanofabricated synthetic pores can mimic transport properties of biological ion channels [P. Yu. Apel, Nucl. Instrum Methods Phys. Res. B 184, 337 (2001); Z. Siwy, Europhys. Lett. 60, 349 (2002)]. Here, the ion current rectification is studied within a reduced one-dimensional (1D) Poisson-Nernst-Planck (PNP) model of synthetic nanopores. A conical channel of a few nm to a few hundred nm in diameter, and of a few mum long is considered in the limit where the channel length considerably exceeds the Debye screening length. The rigid channel wall is assumed to be weakly charged. A one-dimensional reduction of the three-dimensional problem in terms of corresponding entropic effects is put forward. The ion transport is described by the nonequilibrium steady-state solution of the 1D Poisson-Nernst-Planck system within a singular perturbation treatment. An analytic formula for the approximate rectification current in the lowest order perturbation theory is derived. A detailed comparison between numerical results and the singular perturbation theory is presented. The crucial importance of the asymmetry in the potential jumps at the pore ends on the rectification effect is demonstrated. This so constructed 1D theory is shown to describe well the experimental data in the regime of small-to-moderate electric currents.

Modifying the surface charge of single track-etched conical nanopores in polyimide

Chemical modification of nanopore surfaces is of great interest as it means that the surface composition is no longer fixed by the choice of substrate material, even to the point where large biomolecules can be attached to the pore walls. Controlling nanopore transport characteristics is one important application of surface modification which is very relevant given the significant interest in sensors based on the transport of ions and molecules through nanopores. Reported here is a method to change the surface charge polarity of single track-etched conical nanopores in polyimide, which also has the potential to attach more complex molecules to the carboxyl groups on the nanopore walls. These carboxyl groups were converted into terminal amino groups, first by activation with N-(3-dimethylaminopropyl)-N-ethylcarbodiimide (EDC) and N-hydroxysuccinimide (NHS) followed by the covalent coupling of ethylenediamine. This results in a changed surface charge polarity. Regeneration of a carboxyl-terminated surface was also possible, by reaction of the amino groups with succinic anhydride. The success of these reactions was confirmed by measurements of the pore's pH sensitive current-voltage (I-V) characteristics before and after the chemical modification, which depend on surface charge. The permselectivity of the pores also changed accordingly with the modification.

A new drug-sensing paradigm based on ion-current rectification in a conically shaped nanopore

Aims: To utilize the ion-current rectification phenomenon observed for conically shaped nanopores as the basis for designing sensors for drug molecules that adsorb to the walls of the nanopore. Methods: The conically shaped nanopore was prepared by the well-known track-etch method in a polyimide (Kapton) membrane. The ion current flowing through the nanopore was measured as a function of applied transmembrane potential in the presence of the analyte drug molecule, Hoechst 33258. Results: The pore walls in the Kapton membrane are hydrophobic yet have fixed carboxylate groups that give the walls a net negative charge. This fixed anionic surface charge causes the nanopore to rectify the ion current flowing through it. The analyte drug molecule, Hoechst 33258, is cationic yet also hydrophobic. When the membrane is exposed to this molecule, it adsorbs to the pore walls and neutralizes the anionic surface charge, thus lowering the extent of ion-current rectification. The change in rectification is proportional to the concentration of the drug. Conclusions: This nanopore sensor is selective for hydrophobic cations relative to anions, neutral molecules and less hydrophobic cations. Future work will explore ways of augmenting this hydrophobic effect-based selectivity so that more highly selective sensors can be obtained.

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.

Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore

Nanoscale pores have potential to be used as biosensors and are an established tool for analysing the structure and composition of single DNA or RNA molecules. Recently, nanopores have been used to measure the binding of enzymes to their DNA substrates. In this technique, a polynucleotide bound to an enzyme is drawn into the nanopore by an applied voltage. The force exerted on the charged backbone of the polynucleotide by the electric field is used to examine the enzyme-polynucleotide interactions. Here we show that a nanopore sensor can accurately identify DNA templates bound in the catalytic site of individual DNA polymerase molecules. Discrimination among unbound DNA, binary DNA/polymerase complexes, and ternary DNA/polymerase/deoxynucleotide triphosphate complexes was achieved in real time using finite state machine logic. This technique is applicable to numerous enzymes that bind or modify DNA or RNA including exonucleases, kinases and other polymerases.

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.

A method for reproducibly preparing synthetic nanopores for resistive-pulse biosensors

There is increasing interest in using nanopores in synthetic membranes as resistive-pulse sensors for biomedical analytes. Analytes detected with prototype artificial-nanopore biosensors include drugs, DNA, proteins, and viruses. This field is, however, currently in its infancy. A key question that must be addressed in order for such sensors to progress from an interesting laboratory experiment to practical devices is: Can the artificial-nanopore sensing element be reproducibly prepared? We have been evaluating sensors that employ a conically shaped nanopore prepared by the track-etch method as the sensor element. We describe here a new two-step pore-etching procedure that allows for good reproducibility in nanopore fabrication. In addition, we describe a simple mathematical model that allows us to predict the characteristics of the pore produced given the experimental parameters of the two-step etch. This method and model constitute important steps toward developing practical, real-world, artificial-nanopore biosensors.

Chemically modified solid-state nanopores

Nanopores are extremely sensitive single-molecule sensors. Recently, electron beams have been used to fabricate synthetic nanopores in thin solid-state membranes with subnanometer resolution. Here we report a new class of chemically modified nanopore sensors. We describe two approaches for monolayer coating of nanopores: (1) self-assembly from solution, in which nanopores approximately 10 nm diameter can be reproducibly coated, and (2) self-assembly under voltage-driven electrolyte flow, in which we are able to coat 5 nm nanopores. We present an extensive characterization of coated nanopores, their stability, reactivity, and pH response.

Hybridization-modulated ion fluxes through peptide-nucleic-acid- functionalized gold nanotubes. A new approach to quantitative label-free DNA analysis

The inner walls of gold nanotubes, prepared by template synthesis in the nanopores of polycarbonate track etch membranes, have been chemically modified with peptide nucleic acid (PNA) and used for label-free quantification of complementary DNA sequences. Selective binding of DNA to the PNA-modified nanotubes is shown to decrease the flux of optically detected anionic markers through the nanotubes in a concentration-dependent manner. The strong dependence of the biorecognition-modulated ion transport through the nanopores on the ionic strength suggests a dominantly electrostatic exclusion mechanism of the ion flux decrease as a result of DNA binding to the PNA-modified nanopores.

Direct Immobilization of Fab‘ in Nanocapillaries for Manipulating Mass-Limited Samples

Interfacing nanoscale elements into a microfluidic device enables a new range of fluidic manipulations. Nanocapillary array membranes (NCAMs), consisting of thin (5 microm < d < 20 microm) membranes containing arrays of nanometer diameter (10 nm < a < 500 nm) pores, are a convenient method of interfacing vertically separated microchannels in microfluidic devices that allow the external control of analyte transport between microfluidic channels. To add functionality to these nanopores beyond simple fluid transport, here we incorporate an antibody-based molecular recognition element onto the pore surface that allows selective capture, purification, and release of specific analytes from a mixture. The pores are fabricated by electroless plating of gold into the nanopores of an NCAM (Au-NCAM). An antibody is then immobilized on the Au-NCAM via gold-thiol chemistry as a thiolated fragment of antigen-binding (Fab') prepared by direct digestion of the antibody followed by reduction of the disulfide linkage on the hinge region. The successful immobilization and biological activity of the resultant Fab' through this protocol is verified on planar gold by fluorescence microscopy, scanning electron microscopy, and atomic force microscopy. Selective capture and release of human insulin is verified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The relative mass spectral peak intensities for insulin versus nonantigenic peptides increase more than 20-fold after passing through the Fab'-Au-NCAM relative to the control Au-NCAM. The affinity-tagged Au-NCAM can be incorporated into microfluidic devices to allow the concentration, capture, and characterization of analytes in complex mixtures with high specificity.

Asymmetric properties of ion transport in a charged conical nanopore

Recently, the experimentally observed asymmetric properties of ion transport in charged conical nanopores (CCNs) that resemble those in biological ion channels have attracted a lot of attention in theoretical studies in nanotechnology research. In this paper, we report several tactics to study this effect by directly solving the Poisson-Nernst-Planck (PNP) equations. The result shows that PNP equations can indeed quantitatively describe the properties of these nanopores. Based on our numerical solutions, we contribute the rectification effect to ion-enrichment and ion-depletion. A detailed study of length dependence of current indicates that a relatively long length is indispensable for the CCNs to have rectification effect. We suggest that PNP equations and the calculation method could be further used to study other shapes of nanopores.

Solid-state nanopores

The passage of individual molecules through nanosized pores in membranes is central to many processes in biology. Previously, experiments have been restricted to naturally occurring nanopores, but advances in technology now allow artificial solid-state nanopores to be fabricated in insulating membranes. By monitoring ion currents and forces as molecules pass through a solid-state nanopore, it is possible to investigate a wide range of phenomena involving DNA, RNA and proteins. The solid-state nanopore proves to be a surprisingly versatile new single-molecule tool for biophysics and biotechnology.

Solid-state nanopore channels with DNA selectivity

Solid-state nanopores have emerged as possible candidates for next-generation DNA sequencing devices. In such a device, the DNA sequence would be determined by measuring how the forces on the DNA molecules, and also the ion currents through the nanopore, change as the molecules pass through the nanopore. Unlike their biological counterparts, solid-state nanopores have the advantage that they can withstand a wide range of analyte solutions and environments. Here we report solid-state nanopore channels that are selective towards single-stranded DNA (ssDNA). Nanopores functionalized with a 'probe' of hair-pin loop DNA can, under an applied electrical field, selectively transport short lengths of 'target' ssDNA that are complementary to the probe. Even a single base mismatch between the probe and the target results in longer translocation pulses and a significantly reduced number of translocation events. Our single-molecule measurements allow us to measure separately the molecular flux and the pulse duration, providing a tool to gain fundamental insight into the channel-molecule interactions. The results can be explained in the conceptual framework of diffusive molecular transport with particle-channel interactions.

A storable encapsulated bilayer chip containing a single protein nanopore

A robust, portable chip containing a single protein nanopore would be a significant development in the practical application of stochastic sensing technology. Here, we describe a chip in which a single alpha-hemolysin (alphaHL) pore in a planar phospholipid bilayer is sandwiched between two layers of agarose gel. These encapsulated nanopore chips remain functional after storage for weeks. The detection of the second messenger inositol 1,4,5-trisphosphate (IP3) was demonstrated with a chip containing a genetically engineered alphaHL pore as the sensor element.

Nanofluidic diode

We present a nanofluidic diode that at voltage range -5 to +5 V rectifies ion current with degrees of rectification reaching several hundreds. The diode is based on a single asymmetric nanopore whose surface was patterned so that a sharp boundary between positively and negatively charged regions is created. This boundary defines a zone that is enriched with positive and negative ions or creates a depletion zone. The principle of operation of the nanofluidic diode is analogous to that of a bipolar semiconductor diode.

Attoliter-Scale Dispensing in Nanofluidic Channels

As fabrication techniques improve, functional fluidic devices with nanometer scale dimensions are rapidly being developed for chemical analysis. Here, we present fluid dispensing in nanochannels with injection volumes ranging from 42 aL to 4.1 fL. Devices with hybrid poly(dimethylsiloxane) and glass nanochannels, 130 nm deep and 580 nm wide or 130 nm deep and 670 nm wide, were used to evaluate two sample dispensing schemes, modified pinched and gated injections. Electrokinetic transport was achieved by applying up to 10 V directly from an analog output board without amplification, producing modest electric field strengths in the nanochannels (0.2-2 kV/cm) and enabling rapid dispensing and analysis (10-100 ms).

Developing synthetic conical nanopores for biosensing applications

In this review we bring together recent results from our group focused towards the development of biosensors from single conically-shaped artificial nanopores. The nanopores, used in the work presented here, were prepared using the track-etch process. The fabrication of track-etched conical nanopores has been optimized to allow for single nanopores with reproducible dimensions to be prepared. We have also demonstrated techniques that allow for easy and controllable manipulation of nanopore geometry (e.g., cone angle). We will consider the ion transport properties of the conical nanopores and factors that affect these properties. Methods for introducing functions that mimic biological ion channels, such as voltage-gating, into these nanopores will also be addressed. Three prototype sensors developed from single conical nanopores will be presented. In the first two sensors, the single conical nanopores function as resistive-pulse sensors and detect the presence of analytes as current-blockade events in the ion current. The third sensor functions in an on/off mode, much like a ligand-gated ion channel. In the presence of a target analyte, the ion current permanently shuts off.

Multi-nanopore force spectroscopy for DNA analysis

The need for low-cost DNA sequence detection in clinical applications is driving development of new technologies. We demonstrate a method for detection of mutations in a DNA sequence purely by electronic means, and without need for fluorescent labeling. Our method uses an array of nanopores to perform synchronized single-molecule force spectroscopy measurements over many molecules in parallel, yielding detailed information on the kinetics of hundreds of molecule dissociations in a single measurement.

Polymer-modified opal nanopores

The surface of nanopores in opal films, assembled from 205 nm silica spheres, was modified with poly(acrylamide) brushes using surface-initiated atom transfer radical polymerization. The colloidal crystal lattice remained unperturbed by the polymerization. The polymer brush thickness was controlled by polymerization time and was monitored by measuring the flux of redox species across the opal film using cyclic voltammetry. The nanopore size and polymer brush thickness were calculated on the basis of the limiting current change. Polymer brush thickness increased over the course of 26 h of polymerization in a logarithmic manner from 1.3 to 8.5 nm, leading to nanopores as small as 7.5 nm.

Template Synthesized Molecularly Imprinted Polymer Nanotube Membranes for Chemical Separations

In this report, we describe the synthesis of a molecularly imprinted polymer (MIP) nanotube membrane, using a porous anodic alumina oxide (AAO) membrane by surface-initiated atom transfer radical polymerization (ATRP). The use of a MIP nanotube membrane in chemical separations gives the advantage of high affinity and selectivity. Furthermore, because the molecular imprinting technique can be applied to different kinds of target molecules, ranging from small organic molecules to peptides and proteins, such MIP nanotube membranes will considerably broaden the application of nanotube membranes in chemical separations and sensors. This report also shows that the ATRP route is an efficient procedure for the preparation of molecularly imprinted polymers. Furthermore, the ATRP route works well in its formation of MIP nanotubes within a porous AAO membrane. The controllable nature of ATRP allows the growth of a MIP nanotube with uniform pores and adjustable thickness. Thus, using the same route, it is possible to tailor the synthesis of MIP nanotube membranes with either thicker MIP nanotubes for capacity improvement or thinner nanotubes for efficiency improvement.

Estimation of solid phase affinity constants using resistive-pulses from functionalized nanoparticles

This paper describes a method for estimating the solid phase affinity constant of antibodies by using resistive-pulse (Coulter counting) data from spherical nanoparticles that expose antigens. We developed this technique by analyzing data published recently by Saleh, O.A., Sohn, L.L., 2003a. Proc. Natl. Acad. Sci. U.S.A. 100, 820-824. These authors used resistive-pulse sensing to detect an increase in the diameter of streptavidin-functionalized colloids due to the binding of monoclonal anti-streptavidin antibodies. Based on further analysis of their data, we were able to determine the number of antibodies bound to the colloids at various antibody concentrations. This information made it possible to estimate the solid phase affinity constant of the interaction by fitting the data with binding isotherms that describe the binding equilibrium between antibody and antigen. We calculated a value of 2.6x10(8)+/-0.8x10(8) M-1 which is in agreement with the specifications of the supplier of the antibody.

Synthetic ion channels and pores (2004-2005)

This critical review covers synthetic ion channels and pores created between January 2004 and December 2005 comprehensively. The discussion of a rich collection of structural motifs may particularly appeal to organic, biological, supramolecular and polymer chemists. Functions addressed include ion selectivity and molecular recognition, as well as responsiveness to light, heat, voltage and membrane composition. The practical applications involved concern certain topics in medicinal chemistry (antibiotics, drug delivery), catalysis and sensing. An introduction to principles and methods is provided for the non-specialist; some new sources of inspiration from fields beyond chemistry are highlighted.

Control of nanopore wetting by a photochromic spiropyran: a light-controlled valve and electrical switch

By modifying the surface of nanoporous alumina membranes using mixtures of a photochromic spiropyran and hydrophobic molecules, it is possible to control the admission of water into the membrane using light. When the spiropyran is in the thermally stable, relatively hydrophobic closed form, the membrane is not wet by an aqueous solution. Upon exposure to UV light, the spiropyran photoisomerizes to the more polar merocyanine form, allowing water to enter the pores and cross the membrane. Thus, the photosensitive membrane acts as a burst valve, allowing the transport of water and ions across the membrane. If the aqueous solution contains ions, then the membrane acts as an electrical switch; photoisomerization leads to a two-order-of-magnitude increase in ionic conductance, allowing a current to flow across the membrane. Exposure to visible light causes photoisomerization of the merocyanine back to the closed, spiro form, but dewetting of the membrane does not occur spontaneously, due to a high activation barrier.

Blocking of an ion channel by a highly charged drug: modeling the effects of applied voltage, electrolyte concentration, and drug concentration

We present a simple physical model to estimate the blocked pore probability of an ion channel that can be blocked by a highly charged drug in solution. The model is inspired by recent experimental work on the blocking of the PA(63) channel, involved in the anthrax toxin infection, by a highly charged drug [Karginov PNAS 102, 15075 (2005)]. The drug binding to the pore is highly specific but the strong dependence of blocking on the applied voltage and electrolyte concentration suggests that long range electrostatic interactions are important. Since basic electrostatic concepts rather than detailed molecular models are considered, the microscopic details of the channel blocking are ignored, although the model captures most of the qualitative characteristics of the problem.

Biosensing with conically shaped nanopores and nanotubes

In this review we consider recent results from our group that are directed towards developing "smart" synthetic nanopores that can mimic the functions of biological nanopores (transmembrane proteins). We first discuss the preparation and characterization of conical nanopores synthesized using the track-etch process. We then consider the design and function of conical nanopores that can rectify the ionic current that flows through these pores under an applied transmembrane potential. Finally, two types of sensors that we have developed with these conical nanopores are described. The first sensor makes use of molecular recognition elements that are bound to the nanopore mouth to selectively block the nanopore tip, thus detecting the presence of the analyte. The second sensor makes use of conical nanopores in a resistive-pulse type experiment, detecting the analyte via transient blockages in ionic current.

Hydrothermally shrunk alumina nanopores and their application to DNA sensing

Hydrothermal treatment of anodized alumina membranes has been known for years and is believed to seal the pores by transforming aluminium oxide into lower density hydroxides. We demonstrate that, at least for 60 nm diameter pores grown from anodization in oxalic acid at 40 V, the hydrothermal treatment significantly shrinks but does not fully seal the nanopores. The pores shrink to a neck of less than 10 nm in diameter and 2-4 microm in length, in which the diffusion coefficient of ions is five orders of magnitude smaller than in the bulk. Because of a high electrolyte resistance through hydrothermally treated shrunken nanopores, they can be used for electrical sensing applications, as demonstrated using the example of DNA sensing. Hybridization of target DNA with a complementary ssDNA covalently immobilized inside the nanopores causes an increase in impedance by more than 50% while a noncomplementary ssDNA has no measurable effect.

Effect of Crown Ether on Ion Currents through Synthetic Membranes Containing a Single Conically Shaped Nanopore

Ion-current measurements were made on synthetic polymer membranes that contained a single conically shaped nanopore. This entailed placing an electrolyte solution on either side of the membrane, using an electrode placed in each solution to control the transmembrane potential, and measuring the resulting transmembrane ion current. The effect of the crown ether commonly called 18-crown-6 (18C6) on the measured ion current was investigated. Adding 18C6 to the electrolyte solution on one side of a conical nanopore membrane provides a way to rectify the ion current flowing through the nanopore. This chemical rectification is observed only when the cation of the electrolyte is complexed by 18C6 (e.g., K+), and when the mouth diameter of the conical nanopore is of molecular dimensions, in this case approximately 1.5 nm. This chemical rectification can either augment or diminish the inherent electrostatic rectification observed with these small mouth-diameter nanopores. We have interpreted these results using a model based on the formation of a junction potential at the membrane-solution interface. This junction potential arises because the transference number for the K+-18C6 complex in bulk solution is larger than its transference number in the mouth of the conical nanopore.

Detecting single porphyrin molecules in a conically shaped synthetic nanopore

We report here the first example of abiotic resistive-pulse sensing of a molecular (as opposed to a particle or macromolecular) analyte. This was accomplished by using a conically shaped nanopore prepared by the track-etch method as the sensing element. It is possible to sense the molecular analyte because the small diameter opening of the conical nanopore (approximately 4.5 nm) is comparable to the diameter of the analyte molecule (approximately 2 nm).

Effects of biological reactions and modifications on conductance of nanofluidic channels

Conductance characteristics of nanofluidic channels (nanochannels) fall into two regimes: at low ionic concentrations, conductance is governed by surface charge while at high ionic concentrations it is determined by nanochannel geometry and bulk ionic concentration. We used aminosilane chemistry and streptavidin-biotin binding to study the effects of surface reactions on nanochannel conductance at different ionic concentrations. Immobilization of small molecules such as aminosilane or biotin mainly changes surface charge, affecting conductance only in the low concentration regime. However, streptavidin not only modifies surface charge but also occludes part of the channel, resulting in observable conductance changes in both regimes. Our observations reflect the interplay between the competing effects of charge and size of streptavidin on nanochannel conductance.

DNA translocation in inorganic nanotubes

Inorganic nanotubes were successfully integrated with microfluidic systems to create nanofluidic devices for single DNA molecule sensing. Inorganic nanotubes are unique in their high aspect ratio and exhibit translocation characteristics in which the DNA is fully stretched. Transient changes of ionic current indicate DNA translocation events. A transition from current decrease to current enhancement during translocation was observed on changing the buffer concentration, suggesting interplay between electrostatic charge and geometric blockage effects. These inorganic nanotube nanofluidic devices represent a new platform for the study of single biomolecule translocation with the potential for integration into nanofluidic circuits.