Nanopore and Nanochannel Transport Studies

Conformational Dynamics in Aptamer Modulate Neurotransmitter Sensing in Nanopores

This study examines how conformational changes in aptamers affect neurotransmitter sensing in nanopores, showing opposite electronic responses to dopamine and serotonin.

Ready-to-use nanopore platform for ethanolamine quantification using an aptamer-based strand displacement assay.

The paper describes a method to quantify ethanolamine using a nanopore-based strand displacement assay with an ethanolamine-specific aptamer.

Calling the Amino Acid Sequence of a Protein/Peptide from the Nanospectrum Produced by a Sub-nanometer Diameter Pore

The paper develops computational methods to process sub-nanopore nanospectra and predict electrical blockade currents from protein sequences for protein identification.

Chemical probe-based Nanopore Sequencing to Selectively Assess the RNA modifications

This paper introduces a chemical probe-based nanopore sequencing method to selectively assess RNA modifications like inosine and pseudouridine with single-nucleotide resolution.

Lossless end-to-end transport of small molecules through micron-length DNA nanochannels

The paper designs DNA nanochannels that allow small molecules to diffuse through micron-length channels, demonstrating controlled transport between compartments.

Direct detection of RNA repair by nanopore sequencing

The paper identifies unique nanopore sequencing signals from 2'-phosphorylated RNAs, enabling detection of RNA repair events in yeast.

The Functional Nanopore Screen: A Versatile High-throughput Assay to Study and Engineer Protein Nanopores in Escherichia coli

The paper introduces a high-throughput assay called the Functional Nanopore screen to study and engineer protein nanopores in E. coli by measuring Ca2+ influx.

Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing

This paper introduces an extended 11-letter DNA alphabet for data storage, using nanopore readout and neural networks to improve accuracy and density.

Direct detection of RNA modifications and structure using single molecule nanopore sequencing

This paper demonstrates direct detection of RNA modifications and structure using single molecule nanopore sequencing, showing it can identify endogenous and exogenous modifications in rRNA from E. coli and S. cerevisiae.

Membrane activity of a DNA-based ion channel depends on the stability of its double-stranded structure.

This study shows that DNA-based ion channels with continuous backbones form more stable and efficient pores in lipid membranes than those with nicks.

Towards Inferring Nanopore Sequencing Ionic Currents from Nucleotide Chemical Structures

The paper presents a deep learning framework to predict nanopore sequencing ionic currents from nucleotide chemical structures and demonstrates its ability to generalize chemical information for modified nucleotides.

Chop-n-drop: in silico assessment of a novel single-molecule protein fingerprinting method employing fragmentation and nanopore detection

The paper evaluates a nanopore-based method for single-molecule protein identification, showing high accuracy and robustness in simulated conditions.

Multiplexed direct detection of barcoded protein reporters on a nanopore array

This paper introduces a new class of reporter proteins that can be directly detected using nanopore sensors for multiplexed, real-time gene expression tracking.

ENDO-Pore: High-throughput linked-end mapping of single DNA cleavage events using nanopore sequencing

ENDO-Pore maps DNA cleavage events using nanopore sequencing, with CSI identifying cleavage sites, and it was benchmarked with restriction endonucleases and CRISPR Cas12a.

Multiplex single-molecule kinetics of nanopore-coupled polymerases

The paper demonstrates a single-molecule method to screen polymerase variants using nanopore sequencing and barcoding, enabling multiplexed analysis of kinetic properties.

Nanopore Sequencing at Mars, Europa and Microgravity Conditions

This study demonstrates nanopore sequencing functionality under reduced gravity conditions relevant to space exploration, including Mars and icy moons, showing consistent performance across different gravitational environments.

Detection of Base Analogs Incorporated During DNA Replication by Nanopore Sequencing

This paper demonstrates the use of nanopore sequencing to detect thymidine analogs incorporated during DNA replication, enabling high-resolution analysis of replication fork dynamics.

Nanopore sequencing undergoes catastrophic sequence failure at inverted duplicated DNA sequences

The paper identifies that nanopore sequencing fails catastrophically at inverted duplicated DNA sequences, leading to incorrect base calls due to elevated current levels.

Nanopore device-based fingerprinting of RNA oligos and microRNAs enhanced with an Osmium tag.

This paper demonstrates that a nanopore device can distinguish RNA oligos with pyrimidine substitutions tagged with OsBp, enabling two-nucleotide sequence sensing.

Real-Time Selective Sequencing with RUBRIC: Read Until with Basecall and Reference-Informed Criteria

The paper introduces RUBRIC, a real-time selective sequencing method for nanopore sequencing that uses on-line basecalling to align against references and make sequence/reject decisions, showing improved performance on mixed samples.

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

This paper introduces a method to measure DNA replication dynamics on single molecules using nanopore sequencing and applies it to yeast to discover new replication origins.

Nanopore detection of bacterial DNA base modifications

This study improves the detection of m6A in bacterial DNA using nanopore sequencing with a binary classifier, highlighting the importance of read quality and comparing results to PacBio methylation calls.

Repeat expansion and methylation state analysis with nanopore sequencing

This paper develops a Cas12a-based enrichment strategy and algorithm for nanopore sequencing to quantify repeat expansions and their methylation status.

Periodically driven force protein translocation through a α-hemolysin biological nano-pore

The paper uses Langevin molecular dynamics to study protein translocation through an α-hemolysin pore under periodic external forces, finding that time-dependent forces enhance translocation efficiency.

Mapping DNA replication with nanopore sequencing

The paper uses nanopore sequencing and a neural network to identify BrdU-labelled DNA tracts in yeast during replication, showing they align with early-firing origins.

Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning

Chiron is a deep learning model that directly translates nanopore raw signals into DNA sequences without segmentation, achieving high accuracy and speed with minimal training data.

A minimalist approach to protein identification

The paper demonstrates a minimalist method for protein identification using isoelectric point and nanopore measurements, achieving over 90% identification rates across multiple proteomes.

De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing

Base-by-base tests of raw nanopore current, native versus amplified DNA, detect 4mC, 5mC and 6mA without training data, recovering seven methylases' motifs (AUC 0.62–0.97).