ArticleBiophysical journal2012
Single-stranded DNA within nanopores: conformational dynamics and implications for sequencing; a molecular dynamics simulation study.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
- Improving All-Atom Molecular Dynamics Models for Quantitative Prediction of Nanopore Blockade Current.bioRxiv : the preprint server for biology · 2026Article
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- Novel Inhibitors of SARS-CoV-2 RNA Identified through Virtual Screening.Journal of chemical information and modeling · 2024Article
- Sequence-Dependent Orientational Coupling and Electrostatic Attraction in Cation-Mediated DNA-DNA Interactions.Journal of chemical theory and computation · 2023Article
- Tracking Topological and Electronic Effects on the Folding and Stability of Guanine-Deficient RNA G-Quadruplexes, Engineered with a New Computational Tool for De Novo Quadruplex Folding.International journal of molecular sciences · 2022Article
- Switching promotor recognition of phage RNA polymerase in silico along lab-directed evolution path.Biophysical journal · 2022Article
- Comparative structural and dynamics study of free and gRNA-bound FnCas9 and SpCas9 proteins.Computational and structural biotechnology journal · 2022Article
- Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA and Cas2.Biophysical journal · 2021Article
- The Nanopore-Tweezing-Based, Targeted Detection of Nucleobases on Short Functionalized Peptide Nucleic Acid Sequences.Polymers · 2021Article
- Atomic resolution of short-range sliding dynamics of thymine DNA glycosylase along DNA minor-groove for lesion recognition.Nucleic acids research · 2021Article
- Atomistic level characterisation of ssDNA translocation through theComputational and structural biotechnology journal · 2021Article
- Article
- Folding intermediate states of the parallel human telomeric G-quadruplex DNA explored using Well-Tempered Metadynamics.Scientific reports · 2020Article
- Simulations of the 2D self-assembly of tripod-shaped building blocks.Beilstein journal of nanotechnology · 2020Article
- Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase.Nucleic acids research · 2019Article
- Determining selection free energetics from nucleotide pre-insertion to insertion in viral T7 RNA polymerase transcription fidelity control.Nucleic acids research · 2019Article
- An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications.Molecules (Basel, Switzerland) · 2019Review
- A multi-axial RNA joint with a large range of motion promotes sampling of an active ribozyme conformation.Nucleic acids research · 2019Article
- The Role of Lipid Interactions in Simulations of the α-Hemolysin Ion-Channel-Forming Toxin.Biophysical journal · 2018Article
- Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.Journal of chemical theory and computation · 2018Article
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3 authors.
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Abstract
Engineered protein nanopores, such as those based on α-hemolysin from Staphylococcus aureus have shown great promise as components of next-generation DNA sequencing devices. However, before such protein nanopores can be used to their full potential, the conformational dynamics and translocation pathway of the DNA within them must be characterized at the individual molecule level. Here, we employ atomistic molecular dynamics simulations of single-stranded DNA movement through a model α-hemolysin pore under an applied electric field. The simulations enable characterization of the conformations adopted by single-stranded DNA, and allow exploration of how the conformations may impact on translocation within the wild-type model pore and a number of mutants. Our results show that specific interactions between the protein nanopore and the DNA can have a significant impact on the DNA conformation often leading to localized coiling, which in turn, can alter the order in which the DNA bases exit the nanopore. Thus, our simulations show that strategies to control the conformation of DNA within a protein nanopore would be a distinct advantage for the purposes of DNA sequencing.
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