ArticleNature chemistry2012
Hidden complexity in the isomerization dynamics of Holliday junctions.
Article in Nature chemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 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
- Multi-axial DNA origami force spectroscopy reveals hidden dynamics of Holliday junctions.bioRxiv : the preprint server for biology · 2025Article
- Modulating transformation of DNA origami nanoarray via sequence design.Nature communications · 2025Article
- Identical sequences, different behaviors: Protein diversity captured at the single-molecule level.Biophysical journal · 2024Article
- The potential of fluorogenicity for single molecule FRET and DyeCycling.QRB discovery · 2024Review
- Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time.Nucleic acids research · 2023Article
- Exciton delocalization in a fully synthetic DNA-templated bacteriochlorin dimer.Physical chemistry chemical physics : PCCP · 2023Article
- Integration Host Factor Binds DNA Holliday Junctions.International journal of molecular sciences · 2022Article
- Moderate activity of RNA chaperone maximizes the yield of self-spliced pre-RNA in vivo.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Exciton Chirality Inversion in Dye Dimers Templated by DNA Holliday Junction.The journal of physical chemistry letters · 2022Article
- Heterogeneous migration routes of DNA triplet repeat slip-outs.Biophysical reports · 2022Article
- Article
- Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays.Methods (San Diego, Calif.) · 2022Review
- Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction.Molecules (Basel, Switzerland) · 2022Article
- Single-Molecule Sensor for High-Confidence Detection of miRNA.ACS sensors · 2022Article
- Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics.Nucleic acids research · 2022Article
- Can DyeCycling break the photobleaching limit in single-molecule FRET?Nano research · 2022Article
- OB-fold Families of Genome Guardians: A Universal Theme Constructed From the Small β-barrel Building Block.Frontiers in molecular biosciences · 2022Review
- Direct unfolding of RuvA-HJ complex at the single-molecule level.Biophysical journal · 2021Article
- Single-molecule insight into stalled replication fork rescue in Escherichia coli.Nucleic acids research · 2021Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A plausible consequence of the rugged folding energy landscapes inherent to biomolecules is that there may be more than one functionally competent folded state. Indeed, molecule-to-molecule variations in the folding dynamics of enzymes and ribozymes have recently been identified in single-molecule experiments, but without systematic quantification or an understanding of their structural origin. Here, using concepts from glass physics and complementary clustering analysis, we provide a quantitative method to analyse single-molecule fluorescence resonance energy transfer (smFRET) data, thereby probing the isomerization dynamics of Holliday junctions, which display such heterogeneous dynamics over a long observation time (T(obs) ≈ 40 s). We show that the ergodicity of Holliday junction dynamics is effectively broken and that their conformational space is partitioned into a folding network of kinetically disconnected clusters. Theory suggests that the persistent heterogeneity of Holliday junction dynamics is a consequence of internal multiloops with varying sizes and flexibilities frozen by Mg(2+) ions. An annealing experiment using Mg(2+) pulses lends support to this idea by explicitly showing that interconversions between trajectories with different patterns can be induced.
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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.