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 13 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
13 citing papers in PubMed.
- Influence of a Single Deuterium Substitution for Protium on the Frequency Generation of Different-Size Bubbles in IFNA17.International journal of molecular sciences · 2023Article
- Influence of Single Deuterium Replacement on Frequency of Hydrogen Bond Dissociation in IFNA17 under the Highest Critical Energy Range.International journal of molecular sciences · 2022Article
- Homologous basic helix-loop-helix transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism.QRB discovery · 2022Article
- Atomic force microscopy-A tool for structural and translational DNA research.APL bioengineering · 2021Review
- Topological polymorphism of nucleosome fibers and folding of chromatin.Biophysical journal · 2021Review
- Specifically bound BZIP transcription factors modulate DNA supercoiling transitions.Scientific reports · 2020Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- Prototype foamy virus intasome aggregation is mediated by outer protein domains and prevented by protocatechuic acid.Scientific reports · 2019Article
- Mechanisms of Protein Search for Targets on DNA: Theoretical Insights.Molecules (Basel, Switzerland) · 2018Article
- Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles.Nucleic acids research · 2017Article
- Recognition of Local DNA Structures by p53 Protein.International journal of molecular sciences · 2017Review
- Interference between Triplex and Protein Binding to Distal Sites on Supercoiled DNA.Biophysical journal · 2017Article
- Updating Darwin: Information and entropy drive the evolution of life.F1000Research · 2016Article
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.