ArticleBiophysical journal2012
Molecular dynamics of a DNA Holliday junction: the inverted repeat sequence d(CCGGTACCGG)₄.
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 16 papers.
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Who cites it
16 citing papers in PubMed, 23 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
- Overcoming aggregation-induced quenching in DNA-assembled rhodamine dimers.Physical chemistry chemical physics : PCCP · 2025Article
- Site-Specific Investigation of DNA Holliday Junction Dynamics and Structure with 6-Methylisoxanthopterin, a Fluorescent Guanine Analog.bioRxiv : the preprint server for biology · 2024Article
- Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.Journal of chemical information and modeling · 2023Article
- Molecular Dynamic Studies of Dye-Dye and Dye-DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions.International journal of molecular sciences · 2023Article
- Article
- Site-specific investigation of DNA Holliday Junction dynamics and structure with 6-Methylisoxanthopterin, a fluorescent guanine analog.Trends in photochemistry & photobiology · 2023Article
- Molecular dynamics simulations of cyanine dimers attached to DNA Holliday junctions.RSC advances · 2022Article
- Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA.The journal of physical chemistry letters · 2022Article
- Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics.Nucleic acids research · 2022Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- DNA-RNA interactions are critical for chromosome condensation inProceedings of the National Academy of Sciences of the United States of America · 2017Article
- Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments.Scientific reports · 2016Article
- Probing the Ion Binding Site in a DNA Holliday Junction Using Förster Resonance Energy Transfer (FRET).International journal of molecular sciences · 2016Article
- Article
- A unique HMG-box domain of mouse Maelstrom binds structured RNA but not double stranded DNA.PloS one · 2015Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
All-atom molecular dynamics (MD) computer simulations have been applied successfully to duplex DNA structures in solution for some years and found to give close accord with observed results. However, the MD force fields have generally not been parameterized against unusual DNA structures, and their use to obtain dynamical models for this class of systems needs to be independently validated. The four-way junction (4WJ), or Holliday junction, is a dynamic DNA structure involved in central cellular processes of homologous replication and double strand break repair. Two conformations are observed in solution: a planar open-X form (OPN) with a mobile center and four duplex arms, and an immobile stacked-X (STX) form with two continuous strands and two crossover strands, stabilized by high salt conditions. To characterize the accuracy of MD modeling on 4WJ, we report a set of explicit solvent MD simulations of ∼100 ns on the repeat sequence d(CCGGTACCGG)(4) starting from the STX structure (PDB code 1dcw), and an OPN structure built for the same sequence. All 4WJ MD simulations converged to a stable STX structure in close accord with the crystal structure. Our MD beginning in the OPN form converts to the STX form spontaneously at both high and low salt conditions, providing a model for the conformational transition. Thus, these simulations provide a successful account of the dynamical structure of the STX form of d(CCGGTACCGG)(4) in solution, and provide new, to our knowledge, information on the conformational stability of the junction and distribution of counterions in the junction interior.
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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.