ArticleBiophysical journal2008
Profiling the thermodynamic softness of adenoviral promoters.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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
9 citing papers in PubMed.
- DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors.Nucleic acids research · 2024Article
- Bubble Relaxation Dynamics in Homopolymer DNA Sequences.Molecules (Basel, Switzerland) · 2023Article
- Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics.PLoS computational biology · 2013Article
- Specificity and heterogeneity of terahertz radiation effect on gene expression in mouse mesenchymal stem cells.Scientific reports · 2013Article
- DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells.Nucleic acids research · 2012Article
- Article
- Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites.BMC bioinformatics · 2010Article
- A nonlinear dynamic model of DNA with a sequence-dependent stacking term.Nucleic acids research · 2009Article
- Toward a detailed description of the thermally induced dynamics of the core promoter.PLoS computational biology · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
We showed previously that anharmonic DNA dynamical features correlate with transcriptional activity in selected viral promoters, and hypothesized that areas of DNA softness may represent loci of functional significance. The nine known promoters from human adenovirus type 5 were analyzed for inherent DNA softness using the Peyrard-Bishop-Dauxois model and a statistical mechanics approach, using a transfer integral operator. We found a loosely defined pattern of softness peaks distributed both upstream and downstream of the transcriptional start sites, and that early transcriptional regions tended to be softer than late promoter regions. When reported transcription factor binding sites were superimposed on our calculated softness profiles, we observed a close correspondence in many cases, which suggests that DNA duplex breathing dynamics may play a role in protein recognition of specific nucleotide sequences and protein-DNA binding. These results suggest that genetic information is stored not only in explicit codon sequences, but also may be encoded into local dynamic and structural features, and that it may be possible to access this obscured information using DNA dynamics calculations.
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.