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At least 19 recordsLinked to original sources
PubMed2006

Chemical reaction equilibrium in nanoporous materials: NO dimerization reaction in carbon slit nanopores.

We present a molecular-level simulation study of the effects of confinement on chemical reaction equilibrium in nanoporous materials. We use the reaction ensemble Monte Carlo (RxMC) method to investigate the effects of temperature, nanopore size, bulk pressure, and capillary condensation on the nitric oxide dimerization reaction in a model carbon slit nanopore in equilibrium with a bulk reservoir. In addition to the RxMC simulations, we also utilize the molecular-dynamics method to determine self-diffusion coefficients for confined nonreactive mixtures of nitric oxide monomers and dimers at compositions obtained from the RxMC simulations. We analyze the effects of the temperature, nanopore width, bulk pressure, and capillary condensation on the reaction equilibrium with respect to the reaction conversion, fluid structure, and self-diffusion coefficients. We show that the influence of the temperature, nanopore size, and capillary condensation on the confined reaction equilibrium is quite dramatic while the effect of the bulk pressure on the reaction equilibrium in the carbon slit nanopore is only moderate. This work is an extension of previous work by Turner et al. [J. Chem. Phys. 114, 1851 (2001)] on the confined reactive nitric oxide system.

Journal Article↗
PubMed2026

Parallel Analysis of Repeat Expansions: An Updated Clinical Nanopore Cas9-Targeted Sequencing Workflow for Nanopore R10 Flow Cells.

Hereditary ataxias, caused by expansions of short tandem repeats, are difficult to diagnose using traditional PCR and Southern blot methods, which struggle to detect complex repeat expansions and cannot assess repeat interruptions or methylation. An updated Clinical Nanopore Cas9-Targeted Sequencing workflow is presented for analyzing repeat expansions, now compatible with the Oxford Nanopore Technologies R10 flow cell. The workflow incorporates the Oxford Nanopore Technologies wf-human-variation Epi2Me workflow, including the Straglr tool to analyze base-called reads, ensuring compatibility with past, current, and future sequencing chemistries. It expands the number of genes analyzed from 10 to 27 and introduces new gene panels for ataxia, myopathy, neurodegeneration, and amyotrophic lateral sclerosis/motor neuron disease. Validated with Coriell reference and clinical samples, this method improves the analysis of pathogenic repeat expansions, providing deeper insights into repeat structures while addressing the limitations of traditional approaches. In this work, the use of multiplexing, Flongle flow cells, and single-gene targeting were explored as alternatives to panel-based approaches in the Clinical Nanopore Cas9-Targeted Sequencing workflow, finding that only single-gene targeting provides compatibility and reliable performance.

Journal Article↗
PubMed2006

Synchrotron X-ray scattering study of the mechanism of nanopore generation in nanoporous organosilicate thin films imprinted with a reactive six-armed porogen.

In situ grazing incidence small-angle X-ray scattering analysis was successfully performed during the thermal processing of film blends of polymethylsilsesquioxane (PMSSQ) precursor and triethoxysilyl-terminated six-arm poly(epsilon-caprolactone) (mPCL6) porogen. In addition, thermogravimetric analysis of the films was carried out in a nitrogen atmosphere. These measurements provide important information about the structures of the blend films and of the resulting porous films. In particular, they are used in this paper to establish the mechanism of the formation of imprinted pores within the blend films. During the heating run, the sacrificial thermal degradation of the porogen component commenced at 320 degrees C, generating pores in the resulting cured PMSSQ films. Only very limited porogen aggregation occurred during the blend film formation process (spin-coating and subsequent drying), and these porogen aggregates were of relatively small size and narrow size distribution. The observed restriction of the formation of such porogen aggregates was found to result from the favorable hybridization reaction of the porogen's reactive end groups with the reactive functional groups of the PMSSQ precursor, which competes with aggregation via reaction between the porogen molecules. The average radius (or half-size) of the porogen aggregates was in the range 2.45-3.98 nm, depending on the porogen loading (10-40 wt %). The porogen aggregates retained their size and size distribution until thermal degradation, which resulted in the imprinting of nanopores in the cured PMSSQ films with size and size distribution corresponding to those of the porogen aggregates. The porosities of the resulting nanoporous films were in the range 12.4-41.7%, depending on the initial porogen loading.

Membranes, Artificial↗
PubMed2026

Amplification-Free Nanopore Sequencing for Herpesvirus DNA Detection in Intraocular Fluids.

PURPOSE: To evaluate the feasibility of amplification-free nanopore sequencing for detecting herpesvirus DNA in intraocular fluid using multiplex polymerase chain reaction (mPCR)-characterized herpesvirus-positive and herpesvirus-negative samples. DESIGN: Retrospective, single-center, cross-sectional study. PARTICIPANTS: This study included 42 patients with uveitis whose intraocular fluid samples were examined by mPCR, including 20 mPCR-positive samples (all positive for herpesviruses) and 22 mPCR-negative samples. METHODS INTERVENTION OR TESTING: DNA extracted from intraocular fluid samples underwent ligation-based library preparation without whole-genome amplification and was sequenced on the MinION platform with Flongle flow cells for untargeted analysis. Nanopore sequencing results were compared with mPCR findings, and associations between nanopore-derived virus-specific read counts and corresponding herpesvirus DNA copy numbers measured by mPCR were assessed. MAIN OUTCOME MEASURES: Primary outcome measure was concordance between nanopore sequencing and mPCR in herpesvirus species identification. Secondary outcome measures included nanopore sequencing detection rates stratified according to mPCR-measured herpesvirus DNA copy numbers and correlations between nanopore sequencing-derived virus-specific read counts and mPCR-measured herpesvirus DNA copy numbers. RESULTS: Among 20 mPCR-positive intraocular fluid samples, nanopore sequencing identified viral DNA from the same herpesvirus species detected by mPCR in 15 (75.0%), indicating species-level concordance. None of the 22 mPCR-negative samples contained virus-specific reads. Among the 22 herpesvirus targets identified in the 20 mPCR-positive samples, herpesvirus DNA copy numbers measured by mPCR were significantly higher in nanopore-positive than in nanopore-negative targets (P = 0.015). Nanopore detection rates increased with increasing herpesvirus DNA copy numbers measured by mPCR: 3 of 6 targets (50.0%) with <105 copies/mL, 2 of 4 (50.0%) with 105-106 copies/mL, and 12 of 12 (100%) with >106 copies/mL (P = 0.021). Nanopore sequencing-derived virus-specific read counts correlated positively with herpesvirus DNA copy numbers measured by mPCR (r = 0.76, P = 0.0004). CONCLUSIONS: Amplification-free nanopore sequencing demonstrated the feasibility of detecting herpesvirus DNA in intraocular fluid samples, with detection performance dependent on herpesvirus DNA load. This simplified workflow may provide complementary information regarding viral DNA burden in minute ocular samples. FINANCIAL DISCLOSURES: Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Herpesvirus↗
PubMed2026

Applicability of Nanopore-only whole-genome sequencing for Pseudomonas aeruginosa outbreak investigation in the ICU setting: a multicentric study.

UNLABELLED: Pseudomonas aeruginosa outbreaks frequently occur in intensive care units (ICUs). In particular, ICU patients requiring mechanical ventilation are vulnerable to P. aeruginosa ventilator-associated pneumonia, which is associated with high morbidity and mortality. Fast and accurate genotyping during the early stage is crucial to document and manage P. aeruginosa outbreaks at the ICU. In this study, we have evaluated the applicability of Oxford Nanopore whole-genome sequencing (WGS) for outbreak investigation and antimicrobial resistance (AMR) prediction. To evaluate whether a Nanopore-only WGS workflow was able to reproduce Illumina-confirmed transmission clusters, 19 P. aeruginosa isolates from ICUs at UZ Brussels (Belgium) that were previously sequenced with Illumina were sequenced using a Nanopore-only workflow based on the latest V14 chemistry, followed by bioinformatic analysis via BugSeq and MBioSEQ Ridom Typer. Although both bioinformatic platforms showed high concordance between Illumina and Nanopore data, MBioSEQ Ridom Typer yielded the lowest allelic distance (maximum one cgMLST allele), confirming all outbreak clusters. When applying the Nanopore-only workflow to longitudinally collected isolates, low genetic heterogeneity (maximum three cgMLST alleles) was observed between isolates from the same patient. WGS and subsequent outbreak analysis of 65 respiratory P. aeruginosa isolates collected from 38 different ICU patients across six Belgian hospitals during a 9-month period showed no intra- or inter-hospital transmission. When the Nanopore-only WGS data were used to predict AMR, there was high categorical agreement (95%) between AMR genotype and phenotype. These findings highlight the potential of Nanopore WGS as a rapid and accurate tool for outbreak investigation of P. aeruginosa. IMPORTANCE: In recent years, Nanopore sequencing has found its way to clinical laboratories because of its affordability, scalability, and, most importantly, its ability to obtain sequencing results in near-real time. However, despite improved raw read accuracies with the latest generation R10.4.1 flow cells, the question remains whether the achieved accuracy is sufficient for accurate bacterial outbreak investigation, particularly in high-risk settings such as intensive care units (ICUs). In this study, we show that Nanopore-only whole-genome sequencing (WGS) is able to match Illumina-only WGS in terms of accuracy for Pseudomonas aeruginosa outbreak investigation in the ICU setting, although important sequence type-dependent and even strain-specific methylation issues need to be resolved in order to guarantee this accuracy. By providing a fast and accurate workflow for reliable P. aeruginosa outbreak investigation, this study could pave the way for large-scale implementation of Nanopore-only WGS, leading to faster outbreak response times.

Humans↗
PubMed2026

NanoSSL: attention mechanism-based self-supervised learning method for protein identification using nanopores.

MOTIVATION: Nanopores are cutting-edge interdisciplinary tools that can analyze biomolecules at the single-molecule level for many applications, e.g. DNA sequencing. Efforts are underway to extend nanopores to proteomics, including the development of machine learning algorithms for protein sequencing and identification. However, single-molecule data are intrinsically noisy and hard to process. Moreover, the development and performance of machine learning for nanopore is jeopardized by data scarcity. Self-supervised learning is an emerging method that may yield advantages in nanopore scenarios. RESULTS: We propose and experimentally validate Nanopore analysis using Self-Supervised Learning (NanoSSL), a generative self-supervised learning framework based on attention mechanisms for the identification of protein signals from nanopores. Leveraging a two-step approach consisting of self-supervised pre-training and supervised fine-tuning, NanoSSL learns useful feature representations from empirical data to facilitate downstream classification tasks. Inspired by the concept of fragmentation in conventional protein sequencing technologies, during pretraining each translocation event is split into multiple non-overlapping fragments of equal size, some of which are randomly masked and reconstructed using a masked autoencoder. Learning the feature representations of the reconstructed nanopore events facilitates molecular identification in fine-tuning. In this study, we retested a publicly available nanopore multiplexed protein sensing dataset for model iteration, and subsequently measured Alzheimer's disease biomarker A&#x3b2;1-42 using homemade solid-state nanopores. Empirical results indicated NanoSSL achieved an unprecedented performance across four metrics: accuracy, precision, recall, and F1 score, when classifying two mutated A&#x3b2;1-42, E22G and G37R. The self-supervised learning and attention mechanism were verified as the source of performance gains. AVAILABILITY AND IMPLEMENTATION: The main program is available at https://doi.org/10.5281/zenodo.17172822.

Nanopores↗
PubMed2006

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.

Biosensing Techniques↗
PubMed2006

Amphotericin B channels in phospholipid membrane-coated nanoporous silicon surfaces: implications for photovoltaic driving of ions across membranes.

The antimycotic agent amphotericin B (AmB) functions by forming complexes with sterols to form ion channels that cause membrane leakage. When AmB and cholesterol mixed at 2:1 ratio were incorporated into phospholipid bilayer membranes formed on the tip of patch pipettes, ion channel current fluctuations with characteristic open and closed states were observed. These channels were also functional in phospholipid membranes formed on nanoporous silicon surfaces. Electrophysiological studies of AmB-cholesterol mixtures that were incorporated into phospholipid membranes formed on the surface of nanoporous (6.5 nm pore diameter) silicon plates revealed large conductance ion channels ( approximately 300 pS) with distinct open and closed states. Currents through the AmB-cholesterol channels on nanoporous silicon surfaces can be driven by voltage applied via conventional electrical circuits or by photovoltaic electrical potential entirely generated when the nanoporous silicon surface is illuminated with a narrow laser beam. Electrical recordings made during laser illumination of AmB-cholesterol containing membrane-coated nanoporous silicon surfaces revealed very large conductance ion channels with distinct open and closed states. Our findings indicate that nanoporous silicon surfaces can serve as mediums for ion-channel-based biosensors. The photovoltaic properties of nanoporous silicon surfaces show great promise for making such biosensors addressable via optical technologies.

Amphotericin B↗
PubMed2005

Modeling electrochemical deposition inside nanotubes to obtain metal-semiconductor multiscale nanocables or conical nanopores.

Nanocables with a radial metal-semiconductor heterostructure have recently been prepared by electrochemical deposition inside metal nanotubes. First, a bare nanoporous polycarbonate track-etched membrane is coated uniformly with a metal film by electroless deposition. The film forms a working electrode for further deposition of a semiconductor layer that grows radially inside the nanopore when the deposition rate is slow. We propose a new physical model for the nanocable synthesis and study the effects of the deposited species concentration, potential-dependent reaction rate, and nanopore dimensions on the electrochemical deposition. The problem involves both axial diffusion through the nanopore and radial transport to the nanopore surface, with a surface reaction rate that depends on the axial position and the time. This is so because the radial potential drop across the deposited semiconductor layer changes with the layer thickness through the nanopore. Since axially uniform nanocables are needed for most applications, we consider the relative role of reaction and axial diffusion rates on the deposition process. However, in those cases where partial, empty-core deposition should be desirable (e.g., for producing conical nanopores to be used in single nanoparticle detection), we give conditions where asymmetric geometries can be experimentally realized.

Journal Article↗
PubMed2006

Deposition of DNA-functionalized gold nanospheres into nanoporous surfaces.

We report the deposition of DNA-conjugated gold nanospheres into arrays of surface nanopores obtained from hexagonally ordered thin polystyrene-b-poly(methyl methacrylate) (PS-b-PMMA) diblock copolymer films on silicon. The deposition occurs spontaneously from aqueous solution and is driven by either electrostatic interactions or specific DNA hybridization events between the DNA nanospheres and the surface nanopores. To mitigate this spontaneous deposition, we have chemically modified the nanopores with either positively charged aminosilanes or oligonucleotide probe sequences. The deposition of DNA nanospheres into the surface nanopores was characterized by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). We have observed preferential immobilization of individual DNA nanospheres within the nanopores, based on the size matching between the two entities. The inclusion density and selectivity of DNA nanosphere deposition into the surface nanopores was found to depend predominantly on the methods through which the nanoporous surfaces were prepared and chemically functionalized.

DNA↗
PubMed2007

Nanopore sensor for fast label-free detection of short double-stranded DNAs.

Functionalizing surface enhanced the molecular sensing ability of a fabricated nanopore by increasing the translocation duration time for a short double-stranded DNA. The surface of nanopore was derivatized with gamma-aminopropyltriethoxysilane and the positively charged surface attracted DNA molecules when they were in the vicinity of nanopore. The translocation duration time of DNA increased due to the strong electrostatic interaction and it enabled us to detect a short double-stranded DNA (<1 kbp) that is under the size limit of a conventional solid state nanopore sensor. Both 539 and 910 bp double-stranded DNAs were analyzed with the surface functionalized nanopore and their translocation kinetics are presented in this work. The new feature of the surface modified nanopore that can detect short double-stranded DNA molecules could readily be applied for a rapid label-free diagnostic analysis in a Lab-On-a-Chip type DNA sensor.

Biosensing Techniques↗
PubMed2006

Electrostatic-gated transport in chemically modified glass nanopore electrodes.

Electrostatic-gated transport in chemically modified glass nanopore electrodes with orifice radii as small as 15 nm is reported. A single conical-shaped nanopore in glass, with a approximately 1 microm radius Pt disk located at the pore base, is prepared by etching the exposed surface of a glass-sealed Pt nanodisk. The electrochemical response of the nanopore electrode corresponds to diffusion of redox-active species through the nanopore orifice to the Pt microdisk. Silanization of the exterior glass surface with Cl(Me)(2)Si(CH(2))(3)CN and the interior pore surface with EtO(Me)(2)Si(CH(2))(3)NH(2) introduces pH-dependent ion selectivity at the pore orifice, a consequence of the electrostatic interactions between the redox ions and protonated surface amines. Nanopore electrodes with very small pore orifice radii (< approximately 50 nm) display anion permselectively at pH < 4, as demonstrated by electrochemical measurement of transport through the pore orifice. Ion selective transport vanishes at pH > 6 or when the pore radius is significantly larger than the Debye screening length, consistent with the observed ion selectivity resulting from electrostatic interactions. The ability to introduce different surface functionalities to the interior and exterior surfaces of glass nanopores is demonstrated using fluorescence microscopy to monitor the localized covalent attachment of 5- (and 6)-carboxytetramethylrhodamine succinimidyl ester to interior pore surfaces previously silanized with EtO(Me)(2)Si(CH(2))(3)NH(2).

Biosensing Techniques↗
PubMed2006

Nanoporous carbon nanotubes synthesized through confined hydrogen-bonding self-assembly.

We report a simple and direct synthetic method for the preparation of nanoporous carbon nanotubes with larger pores (>10 nm) on the tube wall. The method combines the use of anodic aluminum oxide (AAO) as a template for the tube diameter and block copolymer/carbohydrates self-assembly within thin films confined inside AAO pore channels to form nanopores. It involves coating the AAO inner pore channel surface with block copolymer (polystyrene-co-poly(vinylpyridine)) and carbohydrates in dimethylformamide (DMF) solution. Drying of DMF induced microphase separation of PS-PVP and formation of ordered PS and PVP/carbohydrate domains. Within the coating, the carbohydrates stay specifically only in the pyridine domains surrounding PS domains due to the hydrogen bonding between carbohydrates and pyridine blocks. After carbonization at high temperature (>460 degrees C) in argon, PS was removed, forming the nanopores and carbohydrates, and PVP was carbonized, forming the framework of nanoporous carbon tubes within AAO channels. Removal of AAO led to the formation of individual monodisperse nanoporous carbon nanotubes with a tube wall of approximately 16 nm. The ease with which these nanoporous carbon nanotubes can be fabricated, and the ability to tune tube nanostructures and surface chemistry through the choice of block copolymers used and carbonization temperature, should facilitate investigations of their scope for practical applications.

Journal Article↗
PubMed2005

Biomaterial immobilization in nanoporous carbon molecular sieves: influence of solution pH, pore volume, and pore diameter.

The adsorption of lysozyme (Lz) onto nanoporous carbon molecular sieves with various pore diameters has been studied at different solution pH values. All the adsorption isotherms have successfully been correlated by the Langmuir equation. The amount of adsorbed Lz depends on the solution pH as well as on the specific pore volume and pore diameter of the adsorbents. The maximum adsorption was observed near the isoelectric point of the Lz (pI approximately 11), suggesting that suppression of electric repulsion between the enzymes plays an important role in the adsorption process. Moreover, the amount adsorbed depends on the pore size and pore volume of the nanoporous carbon adsorbents, indicating that the Lz molecules are adsorbed inside the mesopores. CMK-3-150 shows a larger amount of Lz adsorption as compared to CMK-3. The increased Lz adsorption capacity of CMK-3-150 may be due to the larger pore volume and pore diameter as compared to that of CMK-3. The unaltered structural order of the nanoporous adsorbents after the adsorption has been confirmed by the physicochemical characterization techniques such as XRD and N(2) adsorption. In addition, FT-IR spectroscopic studies confirm that the Lz used in this study is stable even after the adsorption on the nanoporous carbon. These results indicate that nanoporous carbon has superior water stability and thus is a more appropriate adsorbent for biomaterials than nanoporous silica.

Adsorption↗
PubMed2005

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.

Crown Ethers↗
PubMed2005

Nanoporous thermosetting polymers.

Potential applications of nanoporous thermosetting polymers include polyelectrolytes in fuel cells, separation membranes, adsorption media, and sensors. Design of nanoporous polymers for such applications entails controlling permeability by tailoring pore size, structure, and interface chemistry. Nanoporous thermosetting polymers are often synthesized via free radical mechanisms using solvents that phase separate during polymerization. In this work, a novel technique for the synthesis of nanoporous thermosets is presented that is based on the reactive encapsulation of an inert solvent using step-growth cross-linking polymerization without micro/macroscopic phase separation. The criteria for selecting such a monomer-polymer-solvent system are discussed based on FTIR analysis, observed micro/macroscopic phase separation, and thermodynamics of swelling. Investigation of resulting network pore structures by scanning electron microscopy (SEM) and small-angle X-ray scattering following extraction and supercritical drying using carbon dioxide showed that nanoporous polymeric materials with pore sizes ranging from 1 to 50 nm can be synthesized by varying the solvent content. The differences in the porous morphology of these materials compared to more common free radically polymerized analogues that exhibit phase separation were evident from SEM imaging. Furthermore, it was demonstrated that the chemical activity of the nanoporous materials obtained by our method could be tailored by grafting appropriate functional groups at the pore interface.

Journal Article↗
PubMed2025

Leveraging basecaller's move table to generate a lightweight k-mer model for nanopore sequencing analysis.

MOTIVATION: Nanopore sequencing by Oxford Nanopore Technologies (ONT) enables direct analysis of DNA and RNA by capturing raw electrical signals. Different nanopore chemistries have varied k-mer lengths, current levels, and standard deviations, which are stored in "k-mer models." In cases where official models are lacking or unsuitable for specific sequencing conditions, tailored k-mer models are crucial to ensure precise signal-to-sequence alignment, analysis and interpretation. The process of transforming raw signal data into nucleotide sequences, known as basecalling, is a fundamental step in nanopore sequencing. RESULTS: In this study, we leverage the move table produced by ONT's basecalling software to create a lightweight de novo k-mer model for RNA004 chemistry. We demonstrate the validity of our custom k-mer model by using it to guide signal-to-sequence alignment analysis, achieving high alignment rates (97.48%) compared to larger default models. Additionally, our 5-mer model exhibits similar performance as the default 9-mer models another analysis, such as detection of m6A RNA modifications. We provide our method, termed Poregen, as a generalizable approach for creation of custom, de novo k-mer models for nanopore signal data analysis. AVAILABILITY AND IMPLEMENTATION: Poregen is an open source package under an MIT license: https://github.com/hiruna72/poregen.

Nanopore Sequencing↗