ArticleThe journal of physical chemistry. C, Nanomaterials and interfaces2012
Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics.
Article in The journal of physical chemistry. C, Nanomaterials and interfaces, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Expandable DNA-origami rings as a nanomechanical platform for studying disordered nucleoporins.bioRxiv : the preprint server for biology · 2026Article
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- High-Rate Fingerprinting of Protein Isoforms by Quasi-regulated Enzyme-free Transport Through CytK Nanopores.Research square · 2026Article
- Transient protein structure guides surface diffusion pathways for electron transport in membrane supercomplexes.Nature communications · 2026Article
- The Brownian dynamics simulator PyRID for reacting and interacting particles written in Python.Cell reports methods · 2025Article
- Molecular permeation through large pore channels: computational approaches and insights.The Journal of physiology · 2025Review
- Enzymes in a human cytoplasm model organize into submetabolon complexes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Modeling Diffusive Motion of Ferredoxin and Plastocyanin on the PSI Domain ofThe journal of physical chemistry. B · 2025Article
- Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Investigating the Quantification Capabilities of a Nanopore-Based Sequencing Platform for Food Safety Application via External Standards of Lambda DNA and Lambda Spiked Beef.Foods (Basel, Switzerland) · 2024Article
- Single-Molecule Detection of the Encounter and Productive Electron Transfer Complexes of a Photosynthetic Reaction Center.Journal of the American Chemical Society · 2024Article
- Single molecule delivery into living cells.Nature communications · 2024Article
- Balancing Group I Monatomic Ion-Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field.Journal of chemical theory and computation · 2024Article
- Leakless end-to-end transport of small molecules through micron-length DNA nanochannels.Science advances · 2022Article
- Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex.Nature communications · 2022Article
- Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations.ACS central science · 2022Article
- Single-molecule biophysics experimentsiScience · 2022Article
- Article
- Anionic Lipids Confine CytochromeBiochemistry · 2022Article
- Multi-resolution simulation of DNA transport through large synthetic nanostructures.Physical chemistry chemical physics : PCCP · 2022Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
It has become possible to distinguish DNA molecules of different nucleotide sequences by measuring ion current passing through a narrow pore containing DNA. To assist experimentalists in interpreting the results of such measurements and to improve the DNA sequence detection method, we have developed a computational approach that has both the atomic-scale accuracy and the computational efficiency required to predict DNA sequence-specific differences in the nanopore ion current. In our Brownian dynamics method, the interaction between the ions and DNA is described by three-dimensional potential of mean force maps determined to a 0.03 nm resolution from all-atom molecular dynamics simulations. While this atomic-resolution Brownian dynamics method produces results with orders of magnitude less computational effort than all-atom molecular dynamics requires, we show here that the ion distributions and ion currents predicted by the two methods agree. Finally, using our Brownian dynamics method, we find that a small change in the sequence of DNA within a pore can cause a large change in the ion current, and validate this result with all-atom molecular dynamics.
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Registered trials
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