ReviewBiophysical reviews2016
Protein/DNA interactions in complex DNA topologies: expect the unexpected.
Review in Biophysical reviews, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed.
- Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.Current opinion in structural biology · 2026Review
- Farnesiferol C enhances the effects of chemotherapy and ionising radiation in human melanoma cells via targeting topoisomerase II alpha.Journal of enzyme inhibition and medicinal chemistry · 2025Article
- Pathways and products of base excision DNA repair in Xenopus laevis eggs: contrast with human cell pathways.Nucleic acids research · 2025Article
- Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning.Biophysical journal · 2024Article
- RNA polymerase efficiently transcribes through DNA-scaffolded, cooperative bacteriophage repressor complexes.FEBS letters · 2022Article
- Atomistic Molecular Dynamics Simulations of DNA in Complex 3D Arrangements for Comparison with Lower Resolution Structural Experiments.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Supercoiling and looping promote DNA base accessibility and coordination among distant sites.Nature communications · 2021Article
- In silico simulations of occurrence of transcription factor binding sites in bacterial genomes.BMC evolutionary biology · 2019Article
- A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry-mass spectrometry.Physical chemistry chemical physics : PCCP · 2017Article
- A review and summary of the contents of biophysical reviews volume 8, 2016.Biophysical reviews · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology.
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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.