ArticleACS nano2012
Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence.
Article in ACS nano, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
35 citing papers in PubMed.
- Improving All-Atom Molecular Dynamics Models for Quantitative Prediction of Nanopore Blockade Current.bioRxiv : the preprint server for biology · 2026Article
- Bioinformatic and computational biophysics tools for nanopore engineering: a review from standard approaches to machine learning advancements.Journal of nanobiotechnology · 2026Review
- Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism.Bioinformatics (Oxford, England) · 2026Article
- Redesign of Translocon EXP2 Nanopore for Detecting Peptide Fragments.Small methods · 2025Article
- Molecular Determinants of Current Blockade Produced by Peptide Transport Through a Nanopore.ACS nanoscience Au · 2024Review
- Article
- Single DNA Translocation and Electrical Characterization Based on Atomic Force Microscopy and Nanoelectrodes.IEEE open journal of nanotechnology · 2022Article
- Controlled movement of ssDNA conjugated peptide throughChemical science · 2021Article
- Recent advances in biological nanopores for nanopore sequencing, sensing and comparison of functional variations in MspA mutants.RSC advances · 2021Review
- Structural-profiling of low molecular weight RNAs by nanopore trapping/translocation using Mycobacterium smegmatis porin A.Nature communications · 2021Article
- Atomistic level characterisation of ssDNA translocation through theComputational and structural biotechnology journal · 2021Article
- The Influence of Electric Field Intensity and Particle Length on the Electrokinetic Transport of Cylindrical Particles Passing through Nanopore.Micromachines · 2020Article
- Nanopore device-based fingerprinting of RNA oligos and microRNAs enhanced with an Osmium tag.Scientific reports · 2019Article
- Controlling the Revolving and Rotating Motion Direction of Asymmetric Hexameric Nanomotor by Arginine Finger and Channel Chirality.ACS nano · 2019Review
- Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage.Nature biotechnology · 2019Article
- An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications.Molecules (Basel, Switzerland) · 2019Review
- Article
- The aerolysin nanopore: from peptidomic to genomic applications.Nanoscale · 2018Review
- Mapping the sensing spots of aerolysin for single oligonucleotides analysis.Nature communications · 2018Article
- Molecular mechanism of DNA association with single-stranded DNA binding protein.Nucleic acids research · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
The protein nanopore Mycobacteria smegmatis porin A (MspA), can be used to sense individual nucleotides within DNA, potentially enabling a technique known as nanopore sequencing. In this technique, single-stranded DNA electrophoretically moves through the nanopore and results in an ionic current that is nucleotide-specific. However, with a high transport velocity of the DNA within the nanopore, the ionic current cannot be used to distinguish signals within noise. Through extensive (~100 μs in total) all-atom molecular dynamics simulations, we examine the effect of positively charged residues on DNA translocation rate and the ionic current blockades in MspA. Simulation of several arginine mutations show a ~10-30 fold reduction of DNA translocation speed without eliminating the nucleotide induced current blockages. Comparison of our results with similar engineering efforts on a different nanopore (α-hemolysin) reveals a nontrivial effect of nanopore geometry on the ionic current blockades in mutant nanopores.
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Registered trials
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