ArticleNucleic acids research2022
Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- 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
- Modulating transformation of DNA origami nanoarray via sequence design.Nature communications · 2025Article
- Detachable DNA Assembly Module to Dissect Tumor Cells Heterogeneity via RNA Pinpoint Screening.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- 3dDNAscoreA: A scoring function for evaluation of DNA 3D structures.Biophysical journal · 2024Article
- Sculpting photoproducts with DNA origami.Chem · 2024Article
- Site-Specific Investigation of DNA Holliday Junction Dynamics and Structure with 6-Methylisoxanthopterin, a Fluorescent Guanine Analog.bioRxiv : the preprint server for biology · 2024Article
- 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
- Site-specific investigation of DNA Holliday Junction dynamics and structure with 6-Methylisoxanthopterin, a fluorescent guanine analog.Trends in photochemistry & photobiology · 2023Article
- Article
- Exciton Chirality Inversion in Dye Dimers Templated by DNA Holliday Junction.The journal of physical chemistry letters · 2022Article
- Article
- Predicting accurate ab initio DNA electron densities with equivariant neural networks.Biophysical journal · 2022Article
- Molecular dynamics simulations of cyanine dimers attached to DNA Holliday junctions.RSC advances · 2022Article
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5 authors.
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Abstract
Immobile four-way junctions (4WJs) are core structural motifs employed in the design of programmed DNA assemblies. Understanding the impact of sequence on their equilibrium structure and flexibility is important to informing the design of complex DNA architectures. While core junction sequence is known to impact the preferences for the two possible isomeric states that junctions reside in, previous investigations have not quantified these preferences based on molecular-level interactions. Here, we use all-atom molecular dynamics simulations to investigate base-pair level structure and dynamics of four-way junctions, using the canonical Seeman J1 junction as a reference. Comparison of J1 with equivalent single-crossover topologies and isolated nicked duplexes reveal conformational impact of the double-crossover motif. We additionally contrast J1 with a second junction core sequence termed J24, with equal thermodynamic preference for each isomeric configuration. Analyses of the base-pair degrees of freedom for each system, free energy calculations, and reduced-coordinate sampling of the 4WJ isomers reveal the significant impact base sequence has on local structure, isomer bias, and global junction dynamics.
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