ArticleBiochemistry2011
Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation.
Article in Biochemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 32 citations in OpenAlex.
- Bioinformatic and computational biophysics tools for nanopore engineering: a review from standard approaches to machine learning advancements.Journal of nanobiotechnology · 2026Review
- Atomistic level characterisation of ssDNA translocation through theComputational and structural biotechnology journal · 2021Article
- An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications.Molecules (Basel, Switzerland) · 2019Review
- The Role of Lipid Interactions in Simulations of the α-Hemolysin Ion-Channel-Forming Toxin.Biophysical journal · 2018Article
- Mapping the sensing spots of aerolysin for single oligonucleotides analysis.Nature communications · 2018Article
- Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore.ACS nano · 2016Article
- DNA sequencing with MspA: Molecular Dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants.Scientific reports · 2015Article
- The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations.Nanomaterials (Basel, Switzerland) · 2015Article
- Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force.Journal of computational chemistry · 2014Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Single-stranded DNA within nanopores: conformational dynamics and implications for sequencing; a molecular dynamics simulation study.Biophysical journal · 2012Article
- Mimicking DNA stretching with the Static Mode method: shear stress versus transverse pulling stress.The European physical journal. E, Soft matter · 2012Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Protein nanopores show great potential as low-cost detectors in DNA sequencing devices. To date, research has largely focused on the staphylococcal pore α-hemolysin (αHL). In the present study, we have developed simplified models of the wild-type αHL pore and various mutants in order to study the translocation dynamics of single-stranded DNA under the influence of an applied electric field. The model nanopores reflect the experimentally measured conductance values in planar lipid bilayers. We show that interactions between rings of cationic amino acids and DNA backbone phosphates result in metastable tethering of nucleic acid molecules within the pore, leading us to propose a "binding and sliding" mechanism for translocation. We also observe folding of DNA into nonlinear conformational intermediates during passage through the confined nanopore environment. Despite adopting nonlinear conformations, the DNA hexamer always exits the pore in the same orientation as it enters (3' to 5') in our simulations. The observations from our simulations help to rationalize experimentally determined trends in residual current and translocation efficiency for αHL and its mutants.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.