ArticleProceedings of the National Academy of Sciences of the United States of America1998
Characterization of the ATF/CREB site and its complex with GCN4.
Article in Proceedings of the National Academy of Sciences of the United States of America, 1998. 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 cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation.Biopolymers · 2015Article
- Rationally designed coiled-coil DNA looping peptides control DNA topology.Nucleic acids research · 2013Article
- Sequence-dependent DNA curvature and flexibility from scanning force microscopy images.Biophysical journal · 2002Article
- Global structure and mechanical properties of a 10-bp nucleosome positioning motif.Proceedings of the National Academy of Sciences of the United States of America · 2000Article
- Bending and adaptability to proteins of the cAMP DNA-responsive element: molecular dynamics contrasted with NMR.Biophysical journal · 2000Article
- Interaction of calicheamicin gamma1(I) and its related carbohydrates with DNA-protein complexes.Proceedings of the National Academy of Sciences of the United States of America · 1999Article
- The SKN-1 amino-terminal arm is a DNA specificity segment.Molecular and cellular biology · 1999Article
- DNA curvature and deformation in protein-DNA complexes: a step in the right direction.Proceedings of the National Academy of Sciences of the United States of America · 1998Review
- DNA-binding domains of Fos and Jun do not induce DNA curvature: an investigation with solution and gel methods.Proceedings of the National Academy of Sciences of the United States of America · 1998Article
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
Abstract
We have studied DNA minicircles containing the ATF/CREB binding site for GCN4 by using a combination of cyclization kinetics experiments and Monte Carlo simulations. Cyclization rates were determined with and without GCN4 for DNA constructs containing the ATF/CREB site separated from a phased A-tract multimer bend by a variable length phasing adaptor. The cyclization results show that GCN4 binding does not significantly change the conformation of the ATF/CREB site, which is intrinsically slightly bent toward the major groove. Monte Carlo simulations quantitate the ATF/CREB site structure as an 8 degrees bend toward the major groove in a coordinate frame near the center of the site. The ATF/CREB site is underwound by 53 degrees relative to the related AP-1 site DNA. The effect of GCN4 binding can be modeled either as a decrease in the local flexibility, corresponding to an estimated 60% increase in the persistence length for the 10-bp binding site, or possibly as a small decrease (1 degrees) in intrinsic bend angle. Our results agree with recent electrophoretic and crystallographic studies and demonstrate that cyclization and simulation can characterize subtle changes in DNA structure and flexibility.
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.