Nanopore membrane-based electrochemical immunoassay

Using nanotechnology in the immunoassay field, Lynntech has developed a nanopore-based sensor with electrochemical signal transduction for the detection of biologically relevant molecular targets. Antibodies of interest were immobilized on the inside wall of nanopores and the antibody–antigen interaction was monitored by measuring the ionic conductance through the nanopores. We have used electrochemical impedance spectroscopy to monitor the changes in the ionic conductance due to the antibody–antigen interaction. To aid the development of a portable, fast immunoassay instrument, we have selected specific impedance frequency values that are very sensitive to the ionic conductance changes. Biomarkers of prostate cancer, prostate-specific antigen and hepsin, were successfully assayed by the nanopore membrane-based electrochemical immunoassay in both phosphate-buffered saline and plasma medium.     

Fabrication of hexagonal boron nitride based 2D nanopore sensor for the assessment of electro-chemical responsiveness of human serum transferrin protein

In this work, we present a step-by-step workflow for the fabrication of 2D hexagonal boron nitride (h-BN) nanopores which are then used to sense holo-human serum transferrin (hSTf) protein at pH ∼8 under applied voltages ranging from +100 mV to +800 mV. 2D nanopores are often used for DNA, however, there is a great void in the literature for single-molecule protein sensing and this, to the best of our knowledge, is the first time where h-BN—a material with large band-gap, low dielectric constant, reduced parasitic capacitance and minimal charge transfer induced noise—is used for protein profiling. The corresponding ΔG (change in pore conductance due to analyte translocation) profiles showed a bimodal Gaussian distribution where the lower and higher ΔG distributions were attributed to (pseudo-) folded and unfolded conformations respectively. With increasing voltage, the voltage induced unfolding increased (evident by decrease in ΔG) and plateaued after ∼400 mV of applied voltage. From the ΔG versus voltage profile corresponding to the pseudo-folded state, we calculated the molecular radius of hSTf, and was found to be ∼3.1 nm which is in close concordance with the literature reported value of ∼3.25 nm.     

Investigating the translocation of λ-DNA molecules through PDMS nanopores

We investigate the translocation of λ-DNA molecules through resistive-pulse polydimethylsiloxane (PDMS) nanopore sensors. Single molecules of λ-DNA were detected as a transient current increase due to the effect of DNA charge on ionic current through the pore. DNA translocation was found to deviate from a Poisson process when the interval between translocations was comparable to the duration of translocation events, suggesting that translocation was impeded during the presence of another translocating molecule in the nanopore. Characterization of translocation at different voltage biases revealed that a critical voltage was necessary to drive DNA molecules through the nanopore. Above this critical voltage, frequency of translocation events was directly proportional to DNA concentration and voltage bias, suggesting that transport of DNA from the solution to the nanopore was the rate limiting step. These observations are consistent with experimental results on transport of DNA through nanopores and nanoslits and the theory of hydrodynamically driven polymer flow in pores.     

Formation of individual protein channels in lipid bilayers suspended in nanopores

Free-standing lipid bilayers are formed in regularly arranged nanopores of 200, 400 and 800 nm in a 300 nm thin hydrophobic silicon nitride membrane separating two fluid compartments. The extraordinary stability of the lipid bilayers allows us to monitor channel formation of the model peptide melittin and α-hemolysin from Staphylococcus aureus using electrochemical impedance spectroscopy and chronoamperometry. We observed that melittin channel formation is voltage-dependent and transient, whereas transmembrane heptameric α-hemolysin channels in nano-BLMs persist for hours. The onset of α-hemolysin-mediated conduction depends on the applied protein concentration and strongly on the diameter of the nanopores. Heptameric channel formation from adsorbed α-hemolysin monomers needs more time in bilayers suspended in 200 nm pores compared to bilayers in pores of 400 and 800 nm diameters. Diffusion of sodium ions across α-hemolysin channels present in a sufficiently high number in the bilayers was quantitatively and specifically determined using ion selective electrodes. The results demonstrate that relatively small variations of nano-dimensions have a tremendous effect on observable dynamic biomolecular processes. Such nanopore chips are potentially useful as supports for stable lipid bilayers to establish functional assays of membrane proteins needed in basic research and drug discovery.     

The effects of electrostatic correlations on the ionic current rectification in conical nanopores

Ion‐ion electrostatic correlations are recognized to play a significant role in the presence of concentrated multivalent electrolytes. To account for their impact on ionic current rectification phenomenon in conical nanopores, we use the modified continuum Poisson‐Nernst‐Planck (PNP) equations by Bazant et al. Coupled with the Stokes equations, the effects of the EOF are also included. We thoroughly investigate the dependence of the ionic current rectification ratios as a function of the double layer thickness and the electrostatic correlation length. By considering the electrostatic correlations, the modified PNP model successfully captures the ionic current rectification reversal in nanopores filled with lanthanum chloride LaCl₃. This finding qualitatively agrees with the experimental observations that cannot be explained by the standard PNP model, suggesting that ion‐ion electrostatic correlations are responsible for this reversal behavior. The modified PNP model not only can be used to explain the experiments, but also go beyond to provide a design tool for nanopore applications involving multivalent electrolytes.     

Protein Detection Through Single Molecule Nanopore

A single nanopore represents a versatile single-molecule probe that can be employed to reveal several important features of proteins, such as physical structure, backbone flexibility, mechanical stability, their folding state, binding affinity to other interacting ligands and enzymatic activity. In this review, we summarize the development and current research related to the field of protein detection by nanopore, as well as a few examples of the pioneer work on protein detection. We first discuss the principle of electrical detection with nanopores and how this technique provides information from current traces. Then the development from peptide detection with biological nanopore to protein detection through solid-state nanopore is described. Finally, we prospect the measurement of protein shape and construction using nanopore technology for the applications in life research area.     

Fabrication and functionalization of nanochannels by electron-beam-induced silicon oxide deposition

We report on the fabrication and electrical characterization of functionalized solid-state nanopores in low stress silicon nitride membranes. First, a pore of approximately 50 nm diameter was drilled using a focused ion beam technique, followed by the local deposition of silicon dioxide. A low-energy electron beam induced the decomposition of adsorbed tetraethyl orthosilicate resulting in site-selective functionalization of the nanopore by the formation of highly insulating silicon oxide. The deposition occurs monolayer by monolayer, which allows for control of the final diameter with subnanometer accuracy. Changes in the pore diameter could be monitored in real time by scanning electron microscopy. Recorded ion currents flowing through a single nanopore revealed asymmetry in the ion conduction properties with the sign of the applied potential. The low-frequency excess noise observed at negative voltage originated from stepwise conductance fluctuations of the open pore.     

Recent progress on nanopore electrochemistry and advanced data processing

Nanopore-based technology offers nanoscale chemical environments with intriguing confinement effects, which isolates individual analytes from the bulk solution. This confined space combines mass transportation and electrochemical measurement, providing new insight into single entity sensing. In this mini-review, we highlight the exciting progress on nanopore electrochemistry. Starting with a concise summary of nanopore-based electrodes, we introduce the fabrication methods and characterizations of the various nanopore electrodes. Then, the special attention focuses on the application of nanopore electrochemistry in single nanoparticle analyzing and intracellular electrochemical sensing. The advanced data analysis tools and Machine Learning algorithms for rapid encoding single-molecule characteristic sets are also covered, which promotes the sensitivity of nanopore electrochemistry and opens a new possibility for revealing single-entity heterogeneity.     

Solid-state nanopores for ion and small molecule analysis

Solid-state nanopore in analytical chemistry has developed rapidly in the 1990s and it is proved to be a versatile new tool for bioanalytical chemistry. The research field of solid-state nanopore starts from mimicking the biological nanopore in living cells. Understanding the transport mechanism of biological nanopore in vivo is a big challenge because of the experimental difficulty, so it is essential to establish the basic research of artificial nanopores in vitro especially for the analysis of ions and small molecules. The performance of solid-state nanopores could be evaluated by monitoring currents when ions and molecules passed through. The comparison of the two types of nanopores based on current-derived information can reveal the principle of biological nanopores, while the solid-state nanopores are applied into practical bioanalysis. In this review, we focus on the researches of the solid-state nanopores in the fabrication process and in the analysis of ions and small molecules. Fabrication methods of nanopores, ion transport mechanism, small molecule analysis and theoretical studies are discussed in detail.     

Chemically-modified nanopores for sensing

Sensing with chemically-modified nanopores is an emerging field that is expected to have major impact on bioanalysis and fundamental understanding of nanoscale chemical interactions down to the single-molecule level. The main strength of nanopore sensing is that it implies the prospect of label-free single-molecule detection by taking advantage of the built-in transport-modulation-based amplification mechanism. At present, fabrication and application of solid-state nanopores are becoming the focus of attention because, compared with their biological counterparts, they offer greater flexibility in terms of shape, size, and surface properties, as well as superior robustness. A breakthrough in label-free nanopore sensing for real-world applications is therefore expected from implementing solid-state nanopores, an area that is still developing. Without claiming comprehensiveness, the focus of this review comprises recent results and trends in nanopore-based sensing (i.e. emerging technologies for fabricating solid-state nanopores, their chemical functionalization, and detection methods for quantitative analysis).     

Electrochemical Quantitative Evaluation of the Surface Charge of a Poly(1-Vinylimidazole) Multilayer Film and Application to Nanopore pH Sensor

Nanopore pH sensing is based on the interaction between the surface charge of the nanopore and ions passing through the nanopore. The nanopore surface charge can be derived from the acid-base dissociation equilibrium of the modified polyelectrolyte. Various polyelectrolytes have been selected based on the acid dissociation constant of the monomer units, and various techniques have been applied to modify nanopores. However, they have been developed without clear guidelines for characterizing the surface modification status or surface charge. One reason has been the difficulty in accurately estimating the surface charge of nanopores in solution. Thus, in this study, the dissociation constant (pKa_app) of the surface charge of a modified polyelectrolyte nanopore was quantitatively estimated via electrochemical measurements. Previously, the modification status of nanopores has been evaluated using the ion current response. In addition, we monitored in real-time the polyelectrolyte modification status using a quartz crystal microbalance (QCM). Some polyelectrolytes were difficult to immobilize directly on the nanopore surface, and those polymers could be effectively modified by the layer-by-layer (LbL) technique. Therefore, we produced a guideline for the fabrication of a nanopore sensor for pH measurements under physiological conditions by quantitative evaluation of the pKa_app via electrochemical methods, the monitoring of the modification status by QCM, and the development of an effective modification method via the LbL technique.     

Discrimination of single‐stranded DNA homopolymers by sieving out G‐quadruplex using tiny solid‐state nanopores

Nanopore sensor has been developed as a promising technology for DNA sequencing at the single‐base resolution. However, the discrimination of homopolymers composed of guanines from other nucleotides has not been clearly revealed due to the easily formed G‐quadruplex in aqueous buffers. In this work, we report that a tiny silicon nitride nanopore was used to sieve out G tetramers to make sure only homopolymers composed of guanines could translocate through the nanopore, then the 20‐nucleotide long ssDNA homopolymers could be identified and differentiated. It is found that the size of the nucleotide plays a major role in affecting the current blockade as well as the dwell time while DNA is translocating through the nanopore. By the comparison of translocation behavior of ssDNA homopolymers composed of nucleotides with different volumes, it is found that smaller nucleotides can lead to higher translocation speed and lower current blockage, which is also found and validated for the 105‐nucleotide long homopolymers. The studies performed in this work will improve our understanding of nanopore‐based DNA sequencing at single‐base level.     

Asymmetric epoxidation of 6-cyano-2,2-dimethylchromene on Mn(salen) catalyst immobilized in mesoporous materials

This article reports our recent work on the heterogeneous asymmetric epoxidation catalyzed by chiral Mn(salen) catalyst axially immobilized via phenoxyl groups and organic sulfonic groups. The asymmetric epoxidation of 6-cyano-2,2-dimethylchromene was especially presented in detail. The factors that affected the asymmetric induction, such as the nanopores and the external surface, the linkage length, and the modification of nanopores with methyl groups were discussed. It was found that the enantioselectivities increased with decreasing the nanopore sizes or increasing the linkage length in nanopore, and the Mn(salen) catalyst immobilized into nanopores generally gave higher ee values than those on the external surface. The heterogeneous Mn(salen) catalysts with modified nanopores gave a TOF of 14.8 h⁻¹ and an ee value of 90.6% for the asymmetric epoxidation of 6-cyano-2,2-dimethylchromene, which were higher than the results (TOF 10.8 h⁻¹, ee 80.1%) obtained for the homogeneous catalyst.     

基于仿生膜的功能化单纳米通道在分析化学中的应用

灵感来源于蛋白质离子通道的仿生功能化单纳米通道,已逐渐成为一种成熟的单分子检测技术和离子整流器。功能化纳米通道包括两种:基因改造的蛋白质纳米通道和固体加工的纳米通道。常用的固体纳米通道有三种:在纳米氮化硅或石墨烯上用聚焦离子束(FIB)或电子束(FEB)轰击得到的纳米通道,化学腐蚀聚合物薄膜中的重金属离子轨迹得到的锥形纳米通道和拉制毛细管或激光刻蚀得到的玻璃纳米孔。相对于蛋白质纳米通道,固态的人工纳米通道具有更优越的机械稳定性,并可用于各种功能基团的修饰。经过近十年的发展,包括蛋白质纳米通道在内的各种仿生的纳米通道已广泛用于对小分子、蛋白质和聚合物等其他一些对象的定性和定量检测。本综述详细介绍了近年来国内外该领域的发展,并对未来的发展方向作了简要的展望。     

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.     

Solid-state nanopores for ion and small molecule analysis

Solid-state nanopore in analytical chemistry has developed rapidly in the 1990s and it is proved to be a versatile new tool for bioanalytical chemistry. This review focuses on the analysis of ions and small molecules with nanopores including nanopipettes, polymer film nanopores, Si₃N₄ nanopores, graphene nanopores, MoS₂ nanopores and MOFs.     

Detection of structured single‐strand DNA via solid‐state nanopore

Nanopore is a single‐molecule analysis method which also employed electrophoresis has achieved promising single‐molecule detections. In this study, we designed two kinds of confined spaces by fabricating solid‐state nanopores with desirable diameters to study the structured single‐strand DNA of C‐rich quadruplex. For the nanopore whose diameter is larger than the quadruplex size, the DNA molecule could directly translocate through the nanopore with extremely high speed. For the nanopore whose diameter is smaller than the quadruplex size, DNA molecule which is captured by nanopore could return to the solution without translocation or unzip the quadruplex structure into single‐strand and then pass the nanopore. This study certifies that choosing a suitable sensing interface is the vital importance of observing detailed single‐molecule information. The solid‐state nanopores hold the great potential to study the structural dynamics of quadruplex DNA molecule.     

Assessment of 1/f noise associated with nanopores fabricated through chemically tuned controlled dielectric breakdown

Recently, we developed a fabrication method—chemically-tuned controlled dielectric breakdown (CT-CDB)—that produces nanopores (through thin silicon nitride membranes) surpassing legacy drawbacks associated with solid-state nanopores (SSNs). However, the noise characteristics of CT-CDB nanopores are largely unexplored. In this work, we investigated the 1/f noise of CT-CDB nanopores of varying solution pH, electrolyte type, electrolyte concentration, applied voltage, and pore diameter. Our findings indicate that the bulk Hooge parameter (α_b) is about an order of magnitude greater than SSNs fabricated by transmission electron microscopy (TEM) while the surface Hooge parameter (α_s) is ∼3 order magnitude greater. Theα_s of CT-CDB nanopores was ∼5 orders of magnitude greater than theirα_b, which suggests that the surface contribution plays a dominant role in 1/f noise. Experiments with DNA exhibited increasing capture rates with pH up to pH ∼8 followed by a drop at pH ∼9 perhaps due to the onset of electroosmotic force acting against the electrophoretic force. The1/f noise was also measured for several electrolytes and LiCl was found to outperform NaCl, KCl, RbCl, and CsCl. The 1/f noise was found to increase with the increasing electrolyte concentration and pore diameter. Taken together, the findings of this work suggest the pH approximate 7–8 range to be optimal for DNA sensing with CT-CDB nanopores.     

Modeling and simulation of nanoparticle separation through a solid-state nanopore

Recent experimental studies show that electrokinetic phenomena such as electroosmosis and electrophoresis can be used to separate nanoparticles on the basis of their size and charge using nanopore‐based devices. However, the efficient separation through a nanopore depends on a number of factors such as externally applied voltage, size and charge density of particle, size and charge density of membrane pore, and the concentration of bulk electrolyte. To design an efficient nanopore‐based separation platform, a continuum‐based mathematical model is used for fluid. The model is based on Poisson–Nernst–Planck equations along with Navier–Stokes equations for fluid flow and on the Langevin equation for particle translocation. Our numerical study reveals that membrane pore surface charge density is a vital parameter in the separation through a nanopore. In this study, we have simulated high‐density lipoprotein (HDL) and low‐density lipoprotein (LDL) as the sample nanoparticles to demonstrate the capability of such a platform. Numerical results suggest that efficient separation of HDL from LDL in a 0.2 M KCL solution (resembling blood buffer) through a 150 nm pore is possible if the pore surface charge density is ～ ?4.0 mC/m². Moreover, we observe that pore length and diameter are relatively less important in the nanoparticle separation process considered here.     

Investigation of entrance effects on particle electrophoretic behavior near a nanopore for resistive pulse sensing

Resistive pulse sensing using solid-state nanopores provides a unique platform for detecting the structure and concentration of molecules of different types of analytes in an electrolyte solution. The capture of an entity into a nanopore is subject not only to the electrostatic force but also the effect of electroosmotic flow originating from the charged nanopore surface. In this study, we theoretically analyze spherical particle electrophoretic behavior near the entrance of a charged nanopore. By investigating the effects of pore size, particle–pore distance, and salt concentration on particle velocity, we summarize dominant mechanisms governing particle behavior for a range of conditions. In the literature, the Helmholtz–Smoluchowski equation is often adopted to evaluate particle translocation by considering the zeta potential difference between the particle and nanopore surfaces. We point out that, due to the difference of the electric field inside and outside the nanopore and the influence from the existence of the particle itself, the zeta potential of the particle, however, needs to be at least 30% higher than that of the nanopore to allow the particle to enter into the nanopore when its velocity is close to zero. Accordingly, we summarize the effective salt concentrations that enable successful particle capture and detection for different pore sizes, offering direct guidance for nanopore applications.