Reversing current rectification to improve DNA‐sensing sensitivity in conical nanopores

Herein, we report the ultrasensitive DNA detection through designing an elegant nanopore biosensor as the first case to realize the reversal of current rectification direction for sensing. Attributed to the unique asymmetric structure, the glass conical nanopore exhibits the sensitive response to the surface charge, which can be facilely monitored by ion current rectification curves. In our design, an enzymatic cleavage reaction was employed to alter the surface charge of the nanopore for DNA sensing. The measured ion current rectification was strongly responsive to DNA concentrations, even reaching to the reversed status from the negative ratio (?6.5) to the positive ratio (+16.1). The detectable concentration for DNA was as low as 0.1 fM. This is an ultrasensitive and label‐free DNA sensing approach, based on the rectification direction‐reversed amplification in a single glass conical nanopore.     

Sensing with ion current rectifying solid-state nanopores

This review gives a current opinion on the state of the art of ion rectifying solid-state nanopore sensors, as well as on the recent directions and challenges of the field, focusing in particular on the progress made in the last two to three years. The review explains the phenomenon of ion current rectification in geometrically asymmetric nanopores and the principle of sensing with these systems. Aside from the conventional approach of analyte immobilization onto the pore surface, some intriguing sensing schemes that decouple the pore selectivity from the surface and promise a more flexible sensing approach are also presented. Lastly, an overview of the recent effort towards amplifying the ion currents and the rectification of these sensors is given, followed by a brief discussion of future perspectives for the field.     

Surface charge density determination of single conical nanopores based on normalized ion current rectification

Current rectification is well known in ion transport through nanoscale pores and channel devices. The measured current is affected by both the geometry and fixed interfacial charges of the nanodevices. In this article, an interesting trend is observed in steady-state current-potential measurements using single conical nanopores. A threshold low-conductivity state is observed upon the dilution of electrolyte concentration. Correspondingly, the normalized current at positive bias potentials drastically increases and contributes to different degrees of rectification. This novel trend at opposite bias polarities is employed to differentiate the ion flux affected by the fixed charges at the substrate-solution interface (surface effect), with respect to the constant asymmetric geometry (volume effect). The surface charge density (SCD) of individual nanopores, an important physical parameter that is challenging to measure experimentally and is known to vary from one nanopore to another, is directly quantified by solving Poisson and Nernst-Planck equations in the simulation of the experimental results. The flux distribution inside the nanopore and the SCD of individual nanopores are reported. The respective diffusion and migration translocations are found to vary at different positions inside the nanopore. This knowledge is believed to be important for resistive pulse sensing applications because the detection signal is determined by the perturbation of the ion current by the analytes.     

A method to tune the ionic current rectification of track-etched nanopores by using surfactant

A method is reported here to tune the ionic current rectification behavior through a conical nanopore fabricated with the track-etching technique. In order to change the surface charge property of the pore wall, we added the cationic surfactant hexadecyl trimethylammonium bromide (CTAB) into the working electrolyte of 0.1 M KCl. By controlling the modified region and the concentration of CTAB, the ionic current rectification degree of the nanopore could be tuned over the wide range of 0.2-65 at the voltage of ±0.9 V. The mechanism of the changes in current rectification behavior was analyzed by numerically solving the Poison-Nernst-Planck (PNP) equations.     

Effect of linear surface-charge non-uniformities on the electrokinetic ionic-current rectification in conical nanopores

The electrokinetic ionic-current rectification in a conical nanopore with linearly varying surface-charge distributions is studied theoretically by using a continuum model composed of a coupled system of the Nernst-Planck equations for the ionic-concentration field and the Poisson equation for the electric potential in the electrolyte solution. The numerical analysis includes the electrochemistry inside reservoirs connected to the nanopore, neglected in previous studies, and more precise accounts of the ionic current are provided. The surface-charge distribution, especially near the tip of the nanopore, significantly affects the ionic enrichment and depletion, which, in turn, influence the resulting ionic current and the rectification. It is shown that non-uniform surface-charge distribution can reverse the direction, or sense, of the rectification. Further insights into the ionic-current rectification are provided by discussing the intriguing details of the electric potential and ionic-concentration fields, leading to the rectification. Rationale for future studies on ionic-current rectification, associated with other non-uniform surface-charge distributions and electroosmotic convection for example, is discussed.     

Modulating ion current rectification generating high energy output in a single glass conical nanopore channel by concentration gradient

Inspired by biological systems that have the inherent skill to generate considerable bioelectricity from the salt content in fluids with highly selective ion channels and pumps on cell membranes,herein,a fully abiotic,single glass conical nanopores energy-harvesting is demonstrated.Ion current rectification(ICR)in negatively charged glass conical nanopores is shown to be controlled by the electrolyte concentration gradient depending on the direction of ion diffusion.The degree of ICR is enhanced with the increasing forward concentration difference.An unusual rectification inversion is observed when the concentration gradient is reversely applied.The maximum power output with the individual nanopore approaches10~4pW.This facile and cost-efficient energy-harvesting system has the potential to power tiny biomedical devices or construct future clean-energy recovery plants.     

The ring opening of substituted cyclopropylidenes to substituted allenes: the effects of steric and long-range electrostatic interactions

Summary It is shown that all stereospecific preferences found experimentally for the ring opening of substituted cyclopropylidenes are satisfactorily reproduced by adding steric and long-range electrostatic interactions to the cyclopropylidene reaction surface. The corresponding surface for dimethyl cyclopropylidene is mapped out in detail. The surface for 3-methyl- and 2-bromo-3-methyl-cyclopropylidene is explored around the transition region. From the success of this approach it is inferred that short-range covalent interactions are unlikely to be responsible for sterospecific preferences found in these systems.Operated for the U.S. Department of Energy by Iowa State University under Contract No. 7405-ENG-82. This work was supported by the office of Basic Energy Sciences     

Electrokinetic properties of monovalent electrolytes confined in charged nanopores: Effect of geometry and ionic short-range correlations

The electrokinetic properties (such as capillary conductance, electroviscosity, and the streaming potential) are obtained for a restricted primitive model electrolyte confined in a slitlike nanopore made up of two infinite parallel plates and in a cylindrical cavity of infinite extension. The hypernetted chain/mean spherical approximation (HNC/MSA) is used to obtain the equilibrium ionic concentration profiles inside the pores, which in turn are used to calculate the electrokinetic properties via linear hydrodynamic equations. Our results are compared with those obtained via the classical Poisson–Boltzmann (PB) theory. Important quantitative and qualitative effects, attributed to geometry and to the proper consideration of short-range correlations by HNC/MSA, are discussed.     

The electrostatical molecular potential — A tool for the prediction of electrostatic molecular interaction properties

Starting from the molecular potential we get, by using elementary electrostatics, information about energetically favoured regions for interaction with ions and dipoles around H₂O and H₂CO. The molecule-dipole interaction is represented by the electric field patterns.     

The effect of screening the electrostatic potentials of reactive sites within B-DNA by metal cations

The effect of screening the backbone phosphates by Mg²⁺ ions, in various ways, on the negative electrostatic potential minima associated with the nucleic acid bases in B-DNA is investigated. The results are compared to screening by Na⁺ ions and to the corresponding potential minima in unscreened B-DNA.     

Molecular surface electrostatic potentials in the analysis of non-hydrogen-bonding noncovalent interactions

Electrostatic potentials computed on molecular surfaces are used to analyse some noncovalent interactions that are not in the category of hydrogen bonding, e.g. “halogen bonding”. The systems examined include halogenated methanes, substituted benzenes,s-tetrazine and l,3-bisphenylurea. The data were obtained byab initio SCF calculations.     

Approximation of the molecular electrostatic potential in a gaussian density functional method

The recently developed Asymptotic Density Model (ADM) [6, 9] is here implemented in the density functional framework using the program deMon-KS [13]. While the original implementation divided the atoms into a core shell and a valence shell, the present version allows for an arbitrary number of shells making it therefore more flexible and, as shown with benzene, potentially more accurate. Moreover, since this method is derived through Poisson's equation, an expression for the electronic charge density is also obtained. However, the present discussion will restrict itself to the electrostatic potential. Finally, even though this method requires parametrization, it is shown that the parameters obtained for homonuclear diatomic species, and used as is in molecular calculations, yield satisfactory results. Indeed, the ADM reproduces almost all basic features of the MEP for all molecules presented here, (water, ammonia, ethylene, acetylene, hydrogen cyanide, carbon monoxide, benzene, nitrous acid). Received: 5 July 1996 / Accepted: 12 November, 1996     

Effect of electrostatic interactions on the formation of proton transfer pathways in human carbonic anhydrase II

We report here a theoretical study on the effect of electrostatic interactions on the formation of dynamical, proton-conducting hydrogen-bonded networks in the protein HCA II. The conformational fluctuations of His-64 is found to contribute crucially to the mechanism of such path formation irrespective of the way electrostatic interactions are modelled.     

The electrostatic molecular potential of yeast tRNAPhe. III. The molecular potential and the steric acessibility associated with the phosphate groups

The molecular electrostatic potential of yeast tRNA^Phe is calculated at sites bridging the anionic oxygens of each of the 76 phosphate groups of the molecule. A quantitative measure of the steric accessibility of the anionic oxygens of the phosphates toward a spherical cation is presented. Both the resulting potentials and accessibilities are discussed in terms of the molecular and electronic structure of tRNA.     

The influence of electrostatic forces on the structure and dynamics of molecular ionic liquids

The vast majority of molecular dynamics simulations are based on nonpolarizable force fields with fixed partial charges for all atoms. The traditional way to obtain these charges are quantum-mechanical calculations performed prior to simulation. Unfortunately, the set of the partial charges heavily relies on the method and the basis set used. Therefore, investigations of the influence of charge variation on simulation data are necessary in order to validate various charge sets. This paper elucidates the consequences of different charge sets on the structure and dynamics of the ionic liquid: 1-ethyl-3-methyl-imidazolium dicyanoamide. The structural features seem to be more or less independent of the partial charge set pointing to a dominance of shape force as modeled by Lennard-Jones parameters. This can be seen in the radial distribution and orientational correlation functions. The role of electrostatic forces comes in when studying dynamical properties. Here, significant deviations between different charge sets can be observed. Overall, dynamics seems to be governed by viscosity. In fact, all dynamical parameters presented in this work can be converted from one charge set to another by viscosity scaling.     

Facile and rapid immobilization of copper(II) bis(oxazoline) catalysts on silica: application to Diels-Alder reactions, recycling, and unexpected effects on enantioselectivity

Two chiral copper(II) bis(oxazoline) complexes have been immobilized on silica via electrostatic interactions using a remarkably straightforward procedure. The immobilized catalysts were tested in a standard Diels-Alder reaction and gave surprising results. Where the immobilized Cu((S,S)-phenyl-box)(OTf)₂ catalyst was used, the predominant enantiomer formed was the opposite of that produced using the same catalyst in a homogeneous reaction. This is a startling result given that the only difference is the electrostatic immobilization of the catalyst on amorphous silica. The activity of the catalyst in a hetero Diels-Alder reaction was also tested. This catalyst was also recycled, successfully maintaining a similar activity to the homogeneous analogue through a number of cycles.     

Role of the electrostatic interactions on the basic or acidic hydrolysis kinetics of poly-( , -lactide) monolayers

The hydrolysis kinetics of insoluble poly-( , -lactide) monolayers spread on basic or acidic aqueous subphase were followed by measuring simultaneously the decrease in the surface area at constant surface pressure and the evolution of the surface potential. An approach to analyse the role of the electrostatic interactions during the hydrolysis at alkaline pH, interpreting the surface potential data was developed. The theoretical predictions based on the idea of a random fragmentation of polymer molecules leading to the interfacial accumulation of charged insoluble products and solubilisation of small fragments describes well the experimental results. The reversibility of the hydrolysis/esterification reaction at acidic pH is taken into account.     

Towards understanding the effect of electrostatic interactions on the density of ionic liquids

In order to have a better understanding on the electrostatic contribution to the thermodynamic property of ionic liquids (ILs), a two-parameter equation of state (EOS) is developed on the basis of hard sphere perturbation theory by accounting for the dispersion interaction with Cotterman et al.’s EOS for L-J fluid and electrostatic interaction with mean spherical approximation (MSA) approach. The EOS is applicable for the density correlation of molecular liquids, and the resulting parameters, viz. Lennard–Jones dispersive parameter ?/k and soft-core diameter σ, can be used to predict the density of molecular mixtures and the corresponding ILs. The results indicate that the density of IL is always about 10% higher than the corresponding stoichiometric molecular mixture with which the IL is produced as an ionic adduct, for example, IL 1-methyl-3-methylimidazolium dimethylphosphate ([MMIM][DMP]) versus equimolar mixture of 1-methylimidazole (MIM) and trimethylphosphate (TMP). Furthermore, the density enhancement of ILs with respect to their corresponding stoichiometric molecular mixtures can be well represented by the electrostatic contribution among ionic species involved.