ArticleProceedings of the National Academy of Sciences of the United States of America2004
Predicting indirect readout effects in protein-DNA interactions.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
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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.
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Who cites it
44 citing papers in PubMed.
- Incorporating Sequence-Dependent DNA Shape and Dynamics into Transcriptome Data Analysis.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif.Biophysical journal · 2022Article
- Host-pathogen protein-nucleic acid interactions: A comprehensive review.Computational and structural biotechnology journal · 2022Review
- The complex architecture of p53 binding sites.Nucleic acids research · 2021Article
- Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes.Nucleic acids research · 2020Article
- Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions.Nature communications · 2019Article
- Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif.Nucleic acids research · 2018Article
- An Evolutionary/Biochemical Connection between Promoter- and Primer-Dependent Polymerases Revealed by Systematic Evolution of Ligands by Exponential Enrichment.Journal of bacteriology · 2018Article
- Article
- Parallels between DNA and collagen - comparing elastic models of the double and triple helix.Scientific reports · 2017Article
- Diverse p53/DNA binding modes expand the repertoire of p53 response elements.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Review
- Interactions of the Metalloregulatory Protein SloR from Streptococcus mutans with Its Metal Ion Effectors and DNA Binding Site.Journal of bacteriology · 2015Article
- Probing a label-free local bend in DNA by single molecule tethered particle motion.Nucleic acids research · 2015Article
- Specific minor groove solvation is a crucial determinant of DNA binding site recognition.Nucleic acids research · 2014Article
- Role of microscopic flexibility in tightly curved DNA.The journal of physical chemistry. B · 2014Article
- Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics.Nature communications · 2014Article
- Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.Nucleic acids research · 2014Article
- DNA dynamics and single-molecule biology.Chemical reviews · 2014Review
- Residue correlation networks in nuclear receptors reflect functional specialization and the formation of the nematode-specific P-box.BMC genomics · 2013Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Recognition of DNA by proteins relies on direct interactions with specific DNA-functional groups, along with indirect effects that reflect variable energetics in the response of DNA sequences to twisting and bending distortions induced by proteins. Predicting indirect readout requires knowledge of the variations in DNA curvature and flexibility in the affected region, which we have determined for a series of DNA-binding sites for the E2 regulatory protein by using the cyclization kinetics method. We examined 16 sites containing different noncontacted spacer sequences, which vary by more than three orders of magnitude in binding affinity. For 15 of these sites, the variation in affinity was predicted within a factor of 3, by using experimental curvature and flexibility values and a statistical mechanical theory. The sole exception was traced to differential magnesium ion binding.
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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.