ArticleNucleic acids research2020
The structural ensemble of a Holliday junction determined by X-ray scattering interference.
Article in Nucleic acids research, 2020. 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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Who cites it
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
- Long-lived pauses reveal tunable kinetic barriers during Holliday junction migration.Nucleic acids research · 2026Article
- Coarse-Grained Modeling and Simulation of Multistranded RNA Nanostars.Chem & bio engineering · 2026Article
- Overcoming the Speed Limit of Four-Way DNA Branch Migration with Bulges in Toeholds.Nano letters · 2025Article
- Modulating transformation of DNA origami nanoarray via sequence design.Nature communications · 2025Article
- Supramolecular Recognition of a DNA Four-Way Junction by an MAngewandte Chemie (International ed. in English) · 2025Article
- Determination of absolute intramolecular distances in proteins using anomalous X-ray scattering interferometry.Nanoscale · 2025Article
- An optofluidic antenna for enhancing the sensitivity of single-emitter measurements.Nature communications · 2024Article
- Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.Journal of chemical information and modeling · 2023Article
- DNA Holliday Junction: History, Regulation and Bioactivity.International journal of molecular sciences · 2022Review
- Visualizing RNA Structures by SAXS-Driven MD Simulations.Frontiers in bioinformatics · 2022Article
- AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation.Nucleic acids research · 2021Article
- Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy.Frontiers in molecular biosciences · 2021Review
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6 authors.
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Abstract
The DNA four-way (Holliday) junction is the central intermediate of genetic recombination, yet key aspects of its conformational and thermodynamic properties remain unclear. While multiple experimental approaches have been used to characterize the canonical X-shape conformers under specific ionic conditions, the complete conformational ensemble of this motif, especially at low ionic conditions, remains largely undetermined. In line with previous studies, our single-molecule Förster resonance energy transfer (smFRET) measurements of junction dynamics revealed transitions between two states under high salt conditions, but smFRET could not determine whether there are fast and unresolvable transitions between distinct conformations or a broad ensemble of related states under low and intermediate salt conditions. We therefore used an emerging technique, X-ray scattering interferometry (XSI), to directly probe the conformational ensemble of the Holliday junction across a wide range of ionic conditions. Our results demonstrated that the four-way junction adopts an out-of-plane geometry under low ionic conditions and revealed a conformational state at intermediate ionic conditions previously undetected by other methods. Our results provide critical information to build toward a full description of the conformational landscape of the Holliday junction and underscore the utility of XSI for probing conformational ensembles under a wide range of solution conditions.
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