ArticleNucleic acids research2018
Sequence-dependent DNA condensation as a driving force of DNA phase separation.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 77 citations in OpenAlex.
- Recent advances in coarse-grained simulations of nucleic acid condensation.The Biochemical journal · 2026Review
- Multivalent cations stabilize DNA duplexes beyond charge neutralization.Chemical science · 2026Article
- Carbon Dots as Electrostatically Driven Base-Selective Chemical Compilers for Programmable Nucleic Acid Condensation.JACS Au · 2026Article
- Imaging and mechanism of DNA-DNA recognition mediated by divalent ions.Nucleic acids research · 2026Article
- Three-color single-molecule fluorescence resonance energy transfer to study macromolecular dynamics.Current opinion in structural biology · 2026Review
- Programmable DNA Folding Modulates Phase Behavior and Dynamics of DNA/Peptide Condensates.ACS nano · 2026Article
- APE1 coordinates its disordered region and metal cofactors to drive genome surveillance.Nucleic acids research · 2026Article
- Alexidine, identified as a Z-DNA inducer by the NanoZ screening platform, acts as a transcriptional regulator.Nucleic acids research · 2026Article
- The emerging sequence grammar of 3D genome organisation.Human genetics · 2025Review
- Protamine Drives Liquid and Solid Condensation of DNA and Glycosaminoglycans.Langmuir : the ACS journal of surfaces and colloids · 2025Article
- Single-molecule measurements of double-stranded DNA condensation.Biophysical journal · 2025Review
- Modeling biomolecular condensates across scales: Atomistic, coarse-grained, and data-driven approaches.Advances in physics: X · 2025Article
- Mechanism of Cationic Lipid Induced DNA Condensation: Lipid-DNA Coordination and Divalent Cation Charge Fluctuations.Biomacromolecules · 2024Article
- Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations.Journal of chemical information and modeling · 2024Article
- Article
- Programming crystallization kinetics of self-assembled DNA crystals with 5-methylcytosine modification.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Pioneer factors: roles and their regulation in development.Trends in genetics : TIG · 2024Review
- Sequence-Dependent Orientational Coupling and Electrostatic Attraction in Cation-Mediated DNA-DNA Interactions.Journal of chemical theory and computation · 2023Article
- Article
- Shelterin Components Modulate Nucleic Acids Condensation and Phase Separation in the Context of Telomeric DNA.Journal of molecular biology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The physical properties of DNA have been suggested to play a central role in spatio-temporal organization of eukaryotic chromosomes. Experimental correlations have been established between the local nucleotide content of DNA and the frequency of inter- and intra-chromosomal contacts but the underlying physical mechanism remains unknown. Here, we combine fluorescence resonance energy transfer (FRET) measurements, precipitation assays, and molecular dynamics simulations to characterize the effect of DNA nucleotide content, sequence, and methylation on inter-DNA association and its correlation with DNA looping. First, we show that the strength of DNA condensation mediated by poly-lysine peptides as a reduced model of histone tails depends on the DNA's global nucleotide content but also on the local nucleotide sequence, which turns out to be qualitatively same as the condensation by spermine. Next, we show that the presence and spatial arrangement of C5 methyl groups determines the strength of inter-DNA attraction, partially explaining why RNA resists condensation. Interestingly, multi-color single molecule FRET measurements reveal strong anti-correlation between DNA looping and DNA-DNA association, suggesting that a common biophysical mechanism underlies them. We propose that the differential affinity between DNA regions of varying sequence pattern may drive the phase separation of chromatin into chromosomal subdomains.
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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.