ArticleJournal of chemical theory and computation2014
A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.
Article in Journal of chemical theory and computation, 2014. 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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Who cites it
38 citing papers in PubMed.
- DNA Nanoarray for Multiplexed RNA Detection With Single-Molecule Readout.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Fitting coarse-grained models to macroscopic experimental data via automatic differentiation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes.Nucleic acids research · 2024Article
- Article
- DNA Volume, Topology, and Flexibility Dictate Nanopore Current Signals.Nano letters · 2023Article
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
- Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions.PLoS computational biology · 2022Article
- Single-molecule biophysics experimentsiScience · 2022Article
- Multi-resolution simulation of DNA transport through large synthetic nanostructures.Physical chemistry chemical physics : PCCP · 2022Review
- Nanopores in Atomically Thin 2D Nanosheets Limit Aqueous Single-Stranded DNA Transport.Physical review letters · 2021Article
- Exploring the most stable aptamer/target molecule complex by the stochastic tunnelling-basin hopping-discrete molecular dynamics method.Scientific reports · 2021Article
- Bottom-Up Coarse-Grained Modeling of DNA.Frontiers in molecular biosciences · 2021Review
- Design Approaches and Computational Tools for DNA Nanostructures.IEEE open journal of nanotechnology · 2021Article
- A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results.Frontiers in molecular biosciences · 2021Review
- High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System.ACS nano · 2020Article
- Streamlining effects of extra telomeric repeat on telomeric DNA folding revealed by fluorescence-force spectroscopy.Nucleic acids research · 2019Article
- Nanomechanics and co-transcriptional folding of Spinach and Mango.Nature communications · 2019Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study.Molecules (Basel, Switzerland) · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
A simple coarse-grained model of single-stranded DNA (ssDNA) was developed, featuring only two sites per nucleotide that represent the centers of mass of the backbone and sugar/base groups. In the model, the interactions between sites are described using tabulated bonded potentials optimized to reproduce the solution structure of DNA observed in atomistic molecular dynamics simulations. Isotropic potentials describe nonbonded interactions, implicitly taking into account the solvent conditions to match the experimentally determined radius of gyration of ssDNA. The model reproduces experimentally measured force-extension dependence of an unstructured DNA strand across 2 orders of magnitude of the applied force. The accuracy of the model was confirmed by measuring the end-to-end distance of a dT
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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.