Effect of single nanoparticle-nanopore interaction strength on ionic current modulation

Solid-state nanopores have been widely used in the detection of biomolecules, but improving DNA sequencing resolution remains a significant challenge. Polyacrylic acid (PAA), known for its abundant carboxyl groups and excellent hydrophilicity, emerges as an ideal material for nanopore sensors. This study, based on molecular dynamics simulations, demonstrates that nanopore sensors incorporating PAA exhibit a "braking" effect. This effect slows down the translocation speed of single-stranded DNA (ssDNA) while enhancing its recognition capability. Findings reveal that a 15% mass fraction of PAA with a polymerization degree of 60 increases the dwell time of ssDNA by approximately 21-fold. In contrast, a 30% mass fraction of PAA with a polymerization degree of 15 extends the ssDNA dwell time by about 30-fold. The addition of a 20% mass fraction PAA with a polymerization degree of 15 significantly increased the dwell times of all ssDNA sequences, with poly(dG)20 showing a notable 20-fold increase. Moreover, the relative current blockage surpassed 0.5 for all ssDNA sequences, with significant variations observed among different sequences. As the polymerization degree or mass fraction of PAA increases, enhanced electrostatic and van der Waals interactions with ssDNA, along with increased hydrogen bond formation, prolong the ssDNA dwell time. Our research demonstrates that PAA effectively enhances the resolution of nanopore DNA sequencing, providing novel insights for developing high-performance nanopore sensors.

We present an instrument capable of performing high-bandwidth (1MHz) solid-state nanopore measurements in a temperature-controlled environment ranging from ambient to 95 °C while maintaining low electrical noise. In previous systems, the ability to control the temperature of the analyte solution during nanopore sensing has come at the expense of significantly greater electrical noise. As a consequence, increased filtering requirements or, equivalently, reduced bandwidths ultimately decrease the utility of such instruments for biosensing applications. Here, we describe in detail the system we have developed that overcomes these difficulties. In particular, we are able to precisely control the temperature of the solution in which a nanopore sensor is immersed by using a closed-loop fluidics system. The ultra-low electrical conductivity heat transfer fluid is used to bring heat from outside of the Faraday cage to the nanopore sensor within the cage, resulting in minimal electrical noise during high-bandwidth measurements while maintaining localized temperature control. As proof-of-concept, we characterize silicon nitride nanopore stability over time at elevated temperatures using electrical measurements and present single-molecule data showing the impact of temperature on capture rate, dwell time, and blockage depth. This tool can unlock the ability to perform a wide range of temperature-sensitive biophysical experiments with solid-state nanopores.

Solid-state nanopore sensors are highly versatile platforms for the rapid, label-free electrical detection and analysis of single molecules, applicable to next generation DNA sequencing. The versatility of this technology allows for both large scale device integration and interfacing with biological systems. Here we report on the development of a hybrid biological solid-state nanopore platform that incorporates a highly mobile lipid bilayer on a single solid-state Al(2)O(3) nanopore sensor, for the potential reconstitution of ion channels and biological nanopores. Such a system seeks to combine the superior electrical, thermal, and mechanical stability of Al(2)O(3) solid-state nanopores with the chemical specificity of biological nanopores. Bilayers on Al(2)O(3) exhibit higher diffusivity than those formed on TiO(2) and SiO(2) substrates, attributed to the presence of a thick hydration layer on Al(2)O(3), a key requirement to preserving the biological functionality of reconstituted membrane proteins. Molecular dynamics simulations demonstrate that the electrostatic repulsion between the dipole of the DOPC headgroup and the positively charged Al(2)O(3) surface may be responsible for the enhanced thickness of this hydration layer. Lipid bilayer coated Al(2)O(3) nanopore sensors exhibit excellent electrical properties and enhanced mechanical stability (GΩ seals for over 50 h), making this technology ideal for use in ion channel electrophysiology, the screening of ion channel active drugs and future integration with biological nanopores such as α-hemolysin and MspA for rapid single molecule DNA sequencing. This technology can find broad application in bio-nanotechnology.

The Finite-Difference Time-Domain (FDTD) modeling technique is applied to study the effect of the cell membrane thickness in optical immersion enhanced phase contrast microscope imaging. The FDTD approach is also applied for studying the implementation of the optical immersion technique for the visualization of single and multiple gold nanoparticles in biological cells. Three different scenarios of biological cells are considered i) with cytoplasm and membrane, ii) with cytoplasm, nucleus and membrane, and iii) with cytoplasm, nucleus, gold nanoparticle(s) and membrane. To the best of our knowledge, this is the first research study using numerical simulations to analyze the effect of cell membrane thickness and single gold nanoparticles on the forward scattered light from biological cells. The results demonstrate the potential of the FDTD modelling approach for biomedical research and extend its applicability to optical immersion technique enhanced nanobiophotonics imaging.

Sensing the Binding Sites of RNAP Holoenzyme on λ DNA Attached to a Probe Tip with Solid State Nanopores

Corrigendum to "Intercomparison of dose enhancement ratio and secondary electron spectra for gold nanoparticles irradiated by X-rays calculated using multiple Monte Carlo simulation codes" [Phys. Med. 69 (2020) 147-163

Penning ionization of propionitrile (CH3CH2C⋮N), acrylonitrile (CH2CHC⋮N), and 3-butenenitrile (CH2CHCH2C⋮N) upon collision with He*(23S) metastable atoms has been studied by two-dimensional Penning ionization electron spectroscopy in which Penning electron intensity is measured as a function of both collision energy and electron energy. We have observed a strong negative collision energy dependence of the partial ionization cross sections for ionization from nonbonding and πCN orbitals of all samples studied, which indicates that the interaction potentials between He*(23S) and target molecules are strongly attractive around the cyano group. For π-conjugated acrylonitrile, strong attractive interaction was shown for the πCC orbital region, while the attractive interaction for the πCC orbital region became weak for nonconjugated 3-butenenitrile. The observed results are consistent with calculated model potential curves. The electron density difference for charge transfer was analyzed for the lone pair orbital region where the molecule acts as an electron donor, while the molecule acts as an electron acceptor for the conjugated π orbital region.

In this paper we model accurately spherical gold nano particle (GNP) excited by plane wave sources. The single GNP behaves as an electromagnetic radiator able to transmit energy in a well defined direction. We study the radiation pattern of a single, double and aligned GNPs by changing different parameters such as the dimensions of the GNP, the working wavelength and the polarization of the source. The radiation pattern is studied by means of a properly designed three dimensional finite element method (FEM) approach.The degeneration of the main lobes and the sensitivity of the radiation pattern are observed by varying different parameters such as the working wavelength and the propagation direction of the source wave vector. As usually observed in nanotechnology, GNPs dimensions are not well defined. For this reason, we study criteria to stabilize the direction of the emitted light by analyzing the light emitted from coupled GNPs. The FEM results are validated by an analytical tool suitable for near field evaluation.

Nanopore sensors have attracted considerable interest for high-throughput sensing of individual nucleic acids and proteins without the need for chemical labels or complex optics. A prevailing problem in nanopore applications is that the transport kinetics of single biomolecules are often faster than the measurement time resolution. Methods to slow down biomolecular transport can be troublesome and are at odds with the natural goal of high-throughput sensing. Here we introduce a low-noise measurement platform that integrates a complementary metal-oxide semiconductor (CMOS) preamplifier with solid-state nanopores in thin silicon nitride membranes. With this platform we achieved a signal-to-noise ratio exceeding five at a bandwidth of 1 MHz, which to our knowledge is the highest bandwidth nanopore recording to date. We demonstrate transient signals as brief as 1 μs from short DNA molecules as well as current signatures during molecular passage events that shed light on submolecular DNA configurations in small nanopores.

Velocity correlations and memory functions in surface diffusion

Solid-state nanopores are nm sized apertures formed in thin synthetic membranes. These single molecule sensors have been used in a variety of biophysical and diagnostic applications and serve as a potential candidate in the development of cost-effective, next generation DNA sequencing technologies, critical to furthering our understanding of inheritance, individuality, disease and evolution. The versatility of solid-state nanopore technology allows for both interfacing with biological systems at the nano-scale as well as large scale VLSI integration promising reliable, affordable, mass producible biosensors with single molecule sensing capabilities. In addition, this technology allows for truly parallel, high throughput DNA and protein analysis through the development of nanopore and micropore arrays in ultra-thin synthetic membranes. This chapter is focused on the development of solid-state nanopore sensors in synthetic membranes and the potential benefits and challenges associated with this technology. Biological nanopores, primarily α-hemolysin and the phi29 connector are also reviewed. We conclude with a detailed discussion on chemically modified solid-state nanopores. These surface functionalized nanopore sensors combine the stability and versatility of solid-state nanopores with the sensitivity and selectivity of biological nanopore systems and may play an important role in drug screening and medical diagnostics.Keywordsα-hemolysinphi29Nanopores in Al2O3 MembranesSurface Charges in NanoporesSurface Enhanced DNA Transport

Protein detection and identification at the single-molecule level are major challenges in many biotechnological fields. Solid-state nanopores have raised attention as label-free biosensors with high sensitivity. Here, we use solid-state nanopore sensing to discriminate two closely related proteins, α-thrombin and γ-thrombin. We show that aptamer functionalization improves protein discrimination thanks to a significant difference in the relative current blockade amplitude. To enhance discrimination, we postprocessed the signals using machine learning and training algorithms and we were able to reach an accuracy of 98.8% using seven features and ensemble methods.

We construct the complete $U\text{\ensuremath{-}}\ensuremath{\mu}$ phase diagram for harmonically confined ultracold fermionic atoms with repulsive and attractive interactions($\ensuremath{\mu}$ is the chemical potential and $U$ the interaction strength). Our approach is based on density-functional theory, and employs analytical expressions for the kinetic and correlation energy functionals, permitting us to obtain closed expressions for all phase boundaries and characteristic lines of the phase diagram, both for repulsive and attractive interactions.

The equilibrium stability of a protein is determined by its amino acid sequence and the solution conditions, such as temperature, pH and presence of chemical denaturant. The stability of a single protein in two identical solutions can nonetheless differ if other macromolecules, termed cosolutes or crowders, are present in one of the solutions at concentrations high enough to occupy a substantial fraction of the solution volume. This effect, due to the presence of the crowders, decreases or increases the stability depending on the interactions between the protein and crowders. Hard-core steric repulsions, which are responsible for the reduction in free volume, are expected to entropically stabilize the protein while attractive interactions can be destabilizing. Here we use a coarse-grained protein model to assess the impact of different types of crowder-protein interactions on the stability of a 35-amino acid model sequence folding into a helical bundle. We find that, for the same interaction strength and concentration, spherical crowders with a hydrophobic character are more destabilizing than crowders interacting nonspecifically with the protein. However, the two types of interactions differ in the degree of association between crowders and protein. At an interaction strength for which the attractive interactions roughly counteracts the stabilizing hard-core repulsions, the nonspecific interactions lead to much stronger crowder-protein association than the hydrophobic interactions. Additionally, we study crowders in the form of polypeptide chains, which are capable of hydrogen bonding with the protein. These peptide crowders have a destabilizing effect even at relatively low crowder concentrations, especially if the sequence of the peptide crowders includes hydrophobic amino acids. Our findings emphasize the importance of the interplay between different types of attractive crowder-protein interactions and entropic effects in determining the net effect on protein stability.

ABSTRACTPolymeric hybrid nanoparticles were synthesized via surface‐initiated atom‐transfer radical polymerization (SI‐ATRP) method on the surface of gold nanoparticles in cyclohexanone. Tetraoctyl ammonium bromide (TOAB) as a phase transfer agent was used to transfer the gold nanoparticles into cyclohexanone, which will be replaced by disulfide initiator on the surface of gold nanoparticles. Transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and UV–vis spectroscopy were utilized to characterize the product to make sure the experiment had been conducted. The results showed that the polymeric gold hybrid nanoparticles with different structures could be controlled by adjusting the ratio of initiator and gold nanoparticles in ATRP. If the ratio is very little, asymmetric polystyrene–gold hybrid nanoparticles were synthesized, and a single gold nanoparticle was attached with a polystyrene sphere. If the ratio becomes larger, core–shell polystyrene–gold nanocomposite particles were obtained resulting in gold nanoparticle encapsulated by a uniform polymer shell. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43584.