Nanopore and Nanochannel Transport Studies

Single-molecule biodosimetry

This paper demonstrates single-molecule biodosimetry using resistive-pulse nanopore sensors to quantify DNA scissions in response to gamma radiation dose.

Sequencing of α-synuclein Intrinsically Disordered Protein in MoS2 Nanopores

This paper uses molecular dynamics simulations to study α-synuclein translocation through MoS2 nanopores, identifying sequence-specific blockade patterns and distinguishing wild-type from mutant proteins.

SMAdd-seq: Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing

The paper introduces SMAdd-seq, a method to profile chromatin accessibility using small molecule intercalation and nanopore sequencing, and demonstrates its application in yeast.

Solid-State Nanopore Sizing for cfDNA Sample Quality Control in Point-of-Need Sequencing

The paper introduces a solid-state nanopore device for label-free cfDNA quality control, showing it correlates with capillary electrophoresis and achieves low measurement variability.

Direct detection of 8-oxo-dG using nanopore sequencing

The paper develops a method to directly detect 8-oxo-dG using nanopore sequencing by creating synthetic DNA with context variability and training deep learning models.

Diffusion of DNA on Atomically Flat 2D Material Surfaces

This study investigates DNA binding and diffusion on hBN surfaces, showing non-specific binding and confinement, and demonstrates potential for nanofluidic biomolecule manipulation.

Brownian motion data augmentation: a method to push neural network performance on nanopore sensors

The paper introduces a Brownian motion data augmentation method to improve neural network performance on nanopore sensors, achieving higher accuracy with a new network architecture.

De Novo Non-Canonical Nanopore Basecalling Enables Private Communication using Heavily-modified DNA Data at Single-Molecule Level

DeepSME enables private DNA-based communication by decrypting heavily modified DNA using nanopore sequencing and deep learning, achieving high precision and recall.

Probe-Free Multiplexed RPA Detection Via Single-Molecule Nanopore Sensing and Deep Learning Classification

This paper develops a probe-free multiplex RPA assay using nanopore sensing and deep learning to classify DNA amplicons, achieving high accuracy for molecular diagnostics.

Hybrid lipid-block copolymer membranes enable stable reconstitution of a wide range of nanopores and robust sampling of serum

This paper demonstrates hybrid polymer-lipid membranes that enable stable nanopore sensing in human serum, showing native-like nanopore behavior and efficient analyte sampling.

Sequencing by Expansion (SBX) -- a novel, high-throughput single-molecule sequencing technology

This paper introduces SBX, a single-molecule sequencing technology that improves nanopore sequencing accuracy and scalability by encoding DNA into Xpandomers with high signal-to-noise reporter codes.

Pneumolysin nanopores with 20 nm inner diameter to characterize the size and shape of Tau oligomers

This paper describes the use of pneumolysin nanopores to characterize the size and shape of Tau oligomers without labeling.

Aerolysin nanopore structure revealed at high resolution in lipid environment

The paper presents high-resolution cryo-EM structures of aerolysin pre-pore and pore in a membrane-like environment, revealing key interactions and constriction rings relevant for nanopore sensing.

ON-OFF nanopores for optical control of transmembrane ionic communication

This paper describes the creation of photopores that switch between iontronic resistor and diode modes using light, enabling optical control of transmembrane ionic communication.

Solid-State Nanopore Real Time Assay for Monitoring Cas9 Endonuclease Reactivity

This paper introduces a polymer electrolyte solid-state nanopore method to monitor endonuclease activity at physiological salt conditions, demonstrating real-time detection of restriction enzyme and CRISPR-Cas9 RNP cleavage.

Charge-based fingerprinting of unlabeled full-length proteins using an aerolysin nanopore

This paper demonstrates the use of an aerolysin nanopore to identify unlabeled full-length proteins through charge-based fingerprinting, achieving 80% accuracy in distinguishing related proteins.

Combining Glycosidases and Nanopore Technology for Glycan Sequencing

This paper demonstrates a glycan sequencing method using glycosidase-assisted nanopore sensing, achieving over 90% accuracy in identifying monosaccharide sequences.

Reversible DNA Translocation as a molecular caliper to probe the nanoscale asymmetry of glass nanopores

This study investigates DNA translocation through conical glass nanopores to quantify how pore asymmetry affects translocation dynamics and sensing length.

Orientation Dependence of Current Blockade in Single Amino Acid Translocation through a Graphene Nanopore

This study investigates how the orientation of single amino acids affects current blockades during translocation through graphene nanopores using molecular dynamics simulations.

Dissecting current rectification through asymmetric nanopores

This study uses molecular dynamics simulations to quantify how voltage-dependent free energy barriers in ion-nanopore systems lead to current rectification, showing it depends on ion type and pore polarity.

Motor protein-assisted glycan translocation and sequencing using nanopores

This paper demonstrates a method for glycan sequencing using nanopores by conjugating glycans to helicase-controlled DNA, achieving reads of up to eleven glycans and enabling controlled translocation and signal detection.

Tuning single-molecule ClyA nanopore tweezers for real-time tracking ofthe conformational dynamics of West Nile viral NS2B/NS3 protease

This study develops a nanopore tweezers platform to track conformational dynamics of West Nile viral NS2B/NS3 protease in real-time and reveals its conformational energy landscape.

Resolving sulfation PTMs on a plant peptide hormone using nanopore sequencing

This study uses nanopore sequencing to accurately detect sulfation and phosphorylation on plant peptide hormones, demonstrating high sensitivity for identifying sulfotyrosine modifications.

De novo design of α-helical peptide channels with designer stoichiometry

This paper designs and characterizes α-helical peptide channels with specific stoichiometry and conductance properties through computational and experimental methods.

Messenger-RNA Modification Standards and Machine Learning Models Facilitate Absolute Site-Specific Pseudouridine Quantification

This paper develops machine learning models to quantitatively measure pseudouridine occupancy in human mRNAs using synthetic controls, revealing site-specific requirements for accurate classification.

A single-molecule nanopore sequencing platform

This paper introduces an improved nanopore sequencing platform called CycloneSEQ, demonstrating long-duration sequencing and high yield with applications in genomics.

Sculpting conducting nanopore size and shape through de novo protein design

This paper designs stable transmembrane beta-barrel nanopores with tailored sizes and shapes using de novo protein design, achieving conductances ranging from 110 pS to 430 pS.

Location of phosphorylation sites within long polypeptide chains by binder-assisted nanopore detection

This study uses nanopore technology with binders to detect and map phosphorylation sites in long polypeptides, advancing nanopore proteomics.

Scaling the Functional Nanopore (FuN) Screen: Systematic Evaluation of Self-Assembling Membrane Peptides and Extension with a K+-Responsive Fluorescent Protein Sensor

The paper evaluates the FuN screen for analyzing self-assembling membrane peptides and extends it with K+-responsive fluorescent protein sensors, benchmarking against traditional biophysical methods.

Efficient 3'-end tailing of RNA with modified adenosine for nanopore direct total RNA sequencing

The paper introduces a method to capture total RNA for nanopore sequencing by modifying 3'-ends with adenosine, enabling detection of both polyadenylated and non-polyadenylated RNAs.