ArticleThe Journal of chemical physics2013
An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization.
Article in The Journal of chemical physics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
99 citing papers in PubMed.
- Simulating Dilute-Solution Properties and Behavior of Flexible Macromolecules: A Review of Brownian Dynamics, Monte Carlo Methods, and Computational Tools (SIMUFLEX and MONTEHYDRO) with Applications to Biomacromolecules and Selected Synthetic Polymers.International journal of molecular sciences · 2026Review
- Visualizing poloidal orientation in DNA minicircles.Biophysical journal · 2026Article
- Exploring functional transitions of the 2'-dG riboswitch aptamer.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.Journal of chemical theory and computation · 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
- Structural organization of HBV pgRNA genome driven by phase separation in capsid confinement.Nature communications · 2026Article
- H4K16 acylations destabilize chromatin architecture and facilitate transcriptional response during metabolic perturbations.Molecular cell · 2026Article
- DNA actively regulates the "safety-belt" dynamics of condensin during loop extrusion.Nature communications · 2026Article
- Nucleosome condensate and linker DNA alter chromatin folding pathways and rates.Biophysical journal · 2026Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.bioRxiv : the preprint server for biology · 2025Article
- Biomolecular Condensates as Emerging Biomaterials: Functional Mechanisms and Advances in Computational and Experimental Approaches.Advanced materials (Deerfield Beach, Fla.) · 2025Review
- Energy Landscapes and Structural Plasticity of Intrinsically Disordered Histones.Journal of chemical information and modeling · 2025Article
- 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.PLoS computational biology · 2025Article
- Article
- Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates.Biochemistry · 2025Review
- Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion.PLoS computational biology · 2025Article
- Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis.The Journal of chemical physics · 2025Article
- Modeling Facilitated Diffusion of Proteins in Crowded Environment.Sub-cellular biochemistry · 2025Review
- Molecular condensation of the CO/NF-YB/NF-YC/FT complex gates floral transition in Arabidopsis.The EMBO journal · 2025Article
- The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle.The Journal of chemical physics · 2024Article
39 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model includes anisotropic potentials between bases involved in base stacking and base pair interactions that enable the description of relevant structural properties, including the major and minor grooves. In an improvement over available coarse-grained models, the correct persistence length is recovered for both ssDNA and dsDNA, allowing for simulation of non-canonical structures such as hairpins. DNA melting temperatures, measured for duplexes and hairpins by integrating over free energy surfaces generated using metadynamics simulations, are shown to be in quantitative agreement with experiment for a variety of sequences and conditions. Hybridization rate constants, calculated using forward-flux sampling, are also shown to be in good agreement with experiment. The coarse-grained model presented here is suitable for use in biological and engineering applications, including nucleosome positioning and DNA-templated engineering.
Indexed as
Identifiers
What OpenQuestion holds
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.