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

Surface coatings for solid-state nanopores

Since their introduction in 2001, solid-state nanopores have been increasingly exploited for the detection and characterization of biomolecules ranging from single DNA strands to protein complexes. A major factor that enables the application of nanopores to the analysis and characterization of a broad range of macromolecules is the preparation of coatings on the pore wall to either prevent non-specific adhesion of molecules or to facilitate specific interactions of molecules of interest within the pore. Surface coatings can therefore be useful to minimize clogging of nanopores or to increase the residence time of target analytes in the pore. This review article describes various coatings and their utility for changing pore diameters, increasing the stability of nanopores, reducing non-specific interactions, manipulating surface charges, enabling interactions with specific target molecules, and reducing the noise of current recordings through nanopores. We compare the coating methods with respect to the ease of preparing the coating, the stability of the coating and the requirement for specialized equipment to prepare the coating.

Wafer-scale fabrication of fused silica chips for low-noise recording of resistive pulses through nanopores

This paper presents a maskless method to manufacture fused silica chips for low-noise resistive-pulse sensing. The fabrication includes wafer-scale density modification of fused silica with a femtosecond-pulsed laser, low-pressure chemical vapor deposition (LPVCD) of silicon nitride (SiN _x ) and accelerated chemical wet etching of the laser-exposed regions. This procedure leads to a freestanding SiN _x window, which is permanently attached to a fused silica support chip and the resulting chips are robust towards Piranha cleaning at ∼80 °C. After parallel chip manufacturing, we created a single nanopore in each chip by focused helium-ion beam or by controlled breakdown. Compared to silicon chips, the resulting fused silica nanopore chips resulted in a four-fold improvement of both the signal-to-noise ratio and the capture rate for signals from the translocation of IgG₁ proteins at a recording bandwidth of 50 kHz. At a bandwidth of ∼1 MHz, the noise from the fused silica nanopore chips was three- to six-fold reduced compared to silicon chips. In contrast to silicon chips, fused silica chips showed no laser-induced current noise-a significant benefit for experiments that strive to combine nanopore-based electrical and optical measurements.

Nanopore-Based, Rapid Characterization of Individual Amyloid Particles in Solution: Concepts, Challenges, and Prospects

Aggregates of misfolded proteins are associated with several devastating neurodegenerative diseases. These so-called amyloids are therefore explored as biomarkers for the diagnosis of dementia and other disorders, as well as for monitoring disease progression and assessment of the efficacy of therapeutic interventions. Quantification and characterization of amyloids as biomarkers is particularly demanding because the same amyloid-forming protein can exist in different states of assembly, ranging from nanometer-sized monomers to micrometer-long fibrils that interchange dynamically both in vivo and in samples from body fluids ex vivo. Soluble oligomeric amyloid aggregates, in particular, are associated with neurotoxic effects, and their molecular organization, size, and shape appear to determine their toxicity. This concept article proposes that the emerging field of nanopore-based analytics on a single molecule and single aggregate level holds the potential to account for the heterogeneity of amyloid samples and to characterize these particles-rapidly, label-free, and in aqueous solution-with regard to their size, shape, and abundance. The article describes the concept of nanopore-based resistive pulse sensing, reviews previous work in amyloid analysis, and discusses limitations and challenges that will need to be overcome to realize the full potential of amyloid characterization on a single-particle level.

Quantitative detection of eryptosis in human erythrocytes using tunable resistive pulse sensing and annexin-V-beads

A novel assay using the quantitative tunable resistive pulse sensing technique to detect eryptosis in human RBCs in a non-optical manner.

Microfluidic-based biosensors toward point-of-care detection of nucleic acids and proteins

This article reviews state-of-the-art microfluidic biosensors of nucleic acids and proteins for point-of-care (POC) diagnostics. Microfluidics is capable of analyzing small sample volumes (10^-9-10^-18 l) and minimizing costly reagent consumption as well as automating sample preparation and reducing processing time. The merger of microfluidics and advanced biosensor technologies offers new promises for POC diagnostics, including high-throughput analysis, portability and disposability. However, this merger also imposes technological challenges on biosensors, such as high sensitivity and selectivity requirements with sample volumes orders of magnitude smaller than those of conventional practices, false response errors due to non-specific adsorption, and integrability with other necessary modules. There have been many prior review articles on microfluidic-based biosensors, and this review focuses on the recent progress in last 5 years. Herein, we review general technologies of DNA and protein biosensors. Then, recent advances on the coupling of the biosensors to microfluidics are highlighted. Finally, we discuss the key challenges and potential solutions for transforming microfluidic biosensors into POC diagnostic applications.

Current oscillations generated by precipitate formation in the mixing zone between two solutions inside a nanopore

Unlike biological protein pores in lipid membranes, nanopores fabricated in synthetic materials can withstand a wide range of environmental conditions including the presence of organic solvents. This capability expands the potential of synthetic nanopores to monitor chemical reactions occurring at the interface between solutions of organic and aqueous character. In this work, nanopores fabricated in borosilicate glass or silicon nitride connected a predominantly organic solvent to an aqueous solvent, thereby generating a mixing zone between these solutions inside the pore. This configuration was exploited to precipitate small organic molecules with low aqueous solubility inside the nanopores, and concomitantly, to monitor this precipitation by the decrease of the ionic conductance through the nanopores over time. Hence, this method provides a means to induce and investigate the formation of nanoprecipitates or nanoparticles. Interestingly, precipitates with a slight electric charge were cleared from the pore, causing the conductance of the pore to return to its original value. This process repeated, resulting in stable oscillations of the ionic current. Although such oscillations might be useful in fluidic logic circuits, few conditions capable of generating oscillations in ionic currents have been reported. The frequency and amplitude of oscillations could be tuned by changing the concentration of the precipitating molecule, the pH of the electrolyte, and the applied potential bias. In addition to generating oscillations, nanopores that separate two different solutions may be useful for monitoring and mediating chemical reactions in the mixing zone between two solutions.

Applications of biological pores in nanomedicine, sensing, and nanoelectronics

Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated - often regulated - functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics.

Toward multiprotein nanoarrays using nanografting and DNA directed immobilization of proteins

Atomic force microscopy nanografting was utilized to prepare DNA nanopatches of different sizes (200 x 200 to 1000 x 1000 nm(2)) onto which DNA-protein conjugates can be anchored through DNA-directed immobilization. Height measurements were used to assess the binding of the proteins as well as their subsequent interaction with other components, such as antibodies. The results indicate that nanografted patch arrays are well suited for application in biosensing and could enable the fabrication of multifeature protein nanoarrays.

Ultrafast laser fabrication of submicrometer pores in borosilicate glass

We demonstrate rapid fabrication of submicrometer-diameter pores in borosilicate glass using femtosecond laser machining and subsequent wet-etch techniques. This approach allows direct and repeatable fabrication of high-quality pores with diameters of 400-800 nm. Such small pores coupled with the desirable electrical and chemical properties of glass enable sensitive resistive-pulse analysis to determine the size and concentration of macromolecules and nanoparticles. Plasma-enhanced chemical vapor deposition allows further reduction of pore diameters to below 300 nm.

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.

Using ion channel-forming peptides to quantify protein-ligand interactions

This paper proposes a method for sensing affinity interactions by triggering disruption of self-assembly of ion channel-forming peptides in planar lipid bilayers. It shows that the binding of a derivative of alamethicin carrying a covalently attached sulfonamide ligand to carbonic anhydrase II (CA II) resulted in the inhibition of ion channel conductance through the bilayer. We propose that the binding of the bulky CA II protein (MW approximately 30 kD) to the ion channel-forming peptides (MW approximately 2.5 kD) either reduced the tendency of these peptides to self-assemble into a pore or extracted them from the bilayer altogether. In both outcomes, the interactions between the protein and the ligand lead to a disruption of self-assembled pores. Addition of a competitive inhibitor, 4-carboxybenzenesulfonamide, to the solution released CA II from the alamethicin-sulfonamide conjugate and restored the current flow across the bilayer by allowing reassembly of the ion channels in the bilayer. Time-averaged recordings of the current over discrete time intervals made it possible to quantify this monovalent ligand binding interaction. This method gave a dissociation constant of approximately 2 microM for the binding of CA II to alamethicin-sulfonamide in the bilayer recording chamber: this value is consistent with a value obtained independently with CA II and a related sulfonamide derivative by isothermal titration calorimetry.