ArticleScientific reports2016
Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments.
Article in Scientific reports, 2016. 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, 21 citations in OpenAlex.
- Multiscale Conformational Dynamics of DNA Holliday Junctions Modulated by Ion Concentration: Insights from Fluorescence Correlation Spectroscopy and Time-Resolved Anisotropy.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Long-lived pauses reveal tunable kinetic barriers during Holliday junction migration.Nucleic acids research · 2026Article
- 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.PLoS computational biology · 2025Article
- Recent progress in probing small molecule interactions with DNA.Biophysical reviews · 2025Review
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Organometallic Pillarplexes That Bind DNA 4-Way Holliday Junctions and Forks.Journal of the American Chemical Society · 2023Article
- Integration Host Factor Binds DNA Holliday Junctions.International journal of molecular sciences · 2022Article
- The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly.Nature communications · 2022Article
- The structural ensemble of a Holliday junction determined by X-ray scattering interference.Nucleic acids research · 2020Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- Coarse-grained modelling of the structural properties of DNA origami.Nucleic acids research · 2019Article
- DNA-RNA interactions are critical for chromosome condensation inProceedings of the National Academy of Sciences of the United States of America · 2017Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Holliday junctions play a central role in genetic recombination, DNA repair and other cellular processes. We combine simulations and experiments to evaluate the ability of the 3SPN.2 model, a coarse-grained representation designed to mimic B-DNA, to predict the properties of DNA Holliday junctions. The model reproduces many experimentally determined aspects of junction structure and stability, including the temperature dependence of melting on salt concentration, the bias between open and stacked conformations, the relative populations of conformers at high salt concentration, and the inter-duplex angle (IDA) between arms. We also obtain a close correspondence between the junction structure evaluated by all-atom and coarse-grained simulations. We predict that, for salt concentrations at physiological and higher levels, the populations of the stacked conformers are independent of salt concentration, and directly observe proposed tetrahedral intermediate sub-states implicated in conformational transitions. Our findings demonstrate that the 3SPN.2 model captures junction properties that are inaccessible to all-atom studies, opening the possibility to simulate complex aspects of junction behavior.
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