ArticleBiophysical journal2013
A model of H-NS mediated compaction of bacterial DNA.
Article in Biophysical journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 31 citations in OpenAlex.
- Temperature-dependent dynamics of DNA methylation and plasmid copy number in Yersinia pestis.BMC genomics · 2026Article
- Modeling the compaction of bacterial chromosomes by biomolecular crowding and the cross-linking protein H-NS.Scientific reports · 2024Article
- Impact of Self-Association on the Architectural Properties of Bacterial Nucleoid Proteins.Biophysical journal · 2021Article
- Requirements for DNA-Bridging Proteins to Act as Topological Barriers of the Bacterial Genome.Biophysical journal · 2020Article
- Bacterial Nucleoid: Interplay of DNA Demixing and Supercoiling.Biophysical journal · 2020Article
- Preferential Localization of the Bacterial Nucleoid.Microorganisms · 2019Article
- Role of Protein Self-Association on DNA Condensation and Nucleoid Stability in a Bacterial Cell Model.Polymers · 2019Article
- Predicting the mechanism and rate of H-NS binding to AT-rich DNA.PLoS computational biology · 2019Article
- Role of Salt Valency in the Switch of H-NS Proteins between DNA-Bridging and DNA-Stiffening Modes.Biophysical journal · 2018Article
- Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins.The Journal of chemical physics · 2018Article
- Mechanism of environmentally driven conformational changes that modulate H-NS DNA-bridging activity.eLife · 2017Article
- Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.Nucleic acids research · 2017Article
- Bacterial Survival under Extreme UV Radiation: A Comparative Proteomics Study ofFrontiers in microbiology · 2017Article
- A model for chromosome organization during the cell cycle in live E. coli.Scientific reports · 2015Article
- Structural change of DNA induced by nucleoid proteins: growth phase-specific Fis and stationary phase-specific Dps.Biophysical journal · 2013Article
- Pack it up, pack it in: unraveling H-NS mediated genome packaging.Biophysical journal · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The histone-like nucleoid structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. H-NS can bind to DNA in two different ways: in trans, by binding to two separate DNA duplexes, or in cis, by binding to different sites on the same duplex. Based on scanning force microscopy imaging and optical trap-driven unzipping assays, it has recently been suggested that DNA compaction may result from the antagonistic effects of H-NS binding to DNA in trans and cis configurations. To get more insight into the compaction mechanism, we constructed a coarse-grained model description of the compaction of bacterial DNA by H-NS. These simulations highlight the fact that DNA compaction indeed results from the subtle equilibrium between several competing factors, which include the deformation dynamics of the plasmid and the several binding modes of protein dimers to DNA, i.e., dangling configurations, cis- and trans-binding. In particular, the degree of compaction is extremely sensitive to the difference in binding energies of the cis and trans configurations. Our simulations also point out that the conformations of the DNA-protein complexes are significantly different in bulk and in planar conditions, suggesting that conformations observed on mica surfaces may differ significantly from those that prevail in living cells.
Indexed as
Identifiers
What OpenQuestion holds
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.