ArticleBiophysical journal2016
Phase Behavior of DNA in the Presence of DNA-Binding Proteins.
Article in Biophysical journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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Who cites it
12 citing papers in PubMed, 27 citations in OpenAlex.
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- The difference of intestinal microbiota composition between Lantang and Landrace newborn piglets.BMC veterinary research · 2023Article
- A sePARate phase? Poly(ADP-ribose) versus RNA in the organization of biomolecular condensates.Nucleic acids research · 2022Review
- The mechanobiology of nuclear phase separation.APL bioengineering · 2022Review
- Facilitated dissociation of nucleoid-associated proteins from DNA in the bacterial confinement.Biophysical journal · 2022Article
- Article
- Spatial Organization of Chromatin: Transcriptional Control of Adaptive Immune Cell Development.Frontiers in immunology · 2021Review
- Visualizing transcription factor dynamics in living cells.The Journal of cell biology · 2018Review
- Role of Condensing Particles in Polymer Confinement: A Model for Virus-Packed "Minichromosomes".Biophysical journal · 2017Article
- Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains.Biophysical journal · 2017Article
- Simulating topological domains in human chromosomes with a fitting-free model.Nucleus (Austin, Tex.) · 2016Article
- Self-Organizing Global Gene Expression Regulated through Criticality: Mechanism of the Cell-Fate Change.PloS one · 2016Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of nonspecific binding proteins, we implemented a Flory-Huggins free energy model. We explored the dependence on DNA and protein concentrations of the DNA collapse. For physiologically relevant values of the DNA-protein affinity, this collapse gives rise to a biphasic regime with a dense and a dilute phase; the corresponding phase diagram was computed. Using an approach based on Hamiltonian paths, we show that the dense phase has either a molten globule or a crystalline structure, depending on the DNA bending rigidity, which is influenced by the ionic strength. These results are valid at the thermodynamical equilibrium and therefore should be consistent with many biological processes, whose characteristic timescales range typically from 1 ms to 10 s. Our model may thus be applied to biological phenomena that involve DNA-binding proteins, such as DNA condensation with crystalline order, which occurs in some bacteria to protect their chromosome from detrimental factors; or transcription initiation, which occurs in clusters called transcription factories that are reminiscent of the dense phase characterized in this study.
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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.