ArticleScience (New York, N.Y.)2013
Probing allostery through DNA.
Article in Science (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 144 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.
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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
144 citing papers in PubMed, 304 citations in OpenAlex.
- Statistical crystallography reveals an allosteric network in SARS-CoV-2 MCommunications biology · 2026Article
- Mechanisms of gene regulation by SRCAP and H2A.Z.Nature communications · 2026Article
- Interplay between circadian and other transcription factors-Implications for cycling transcriptome reprogramming.FEBS letters · 2026Review
- Article
- Molecular Cloning, Optimization of Expression and Functional Characterization of the Global Transcriptional Regulator MosR (Rv0348) of Mycobacterium tuberculosis.Applied biochemistry and biotechnology · 2025Article
- Mechanisms driving functional divergence of transcription factor paralogs.The New phytologist · 2025Review
- Long-Range Allosteric Modulation of DNA Duplex Dynamics Induced by Pyrrole-Imidazole Polyamide Binding.The journal of physical chemistry letters · 2025Article
- Exploring Abeta42 monomer diffusion dynamics on fibril surfaces through molecular simulations.Protein science : a publication of the Protein Society · 2025Article
- Quantification and potential functional relevance of binding cooperativity of adjacent transcription factors on DNA.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- DNA-Protein Binding is Dominated by Short Anchoring Elements.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Cytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14.International journal of molecular sciences · 2025Article
- Improving the use of CRISPR/Cas9 gene editing machinery as a cancer therapeutic tool with the help of nanomedicine.3 Biotech · 2025Review
- Genome-wide single-cell and single-molecule footprinting of transcription factors with deaminase.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Advances of Predicting Allosteric Mechanisms Through Protein Contact in New Technologies and Their Application.Molecular biotechnology · 2024Review
- Stacking correlation length in single-stranded DNA.Nucleic acids research · 2024Article
- A DNA base-specific sequence interposed between CRX and NRL contributes to RHODOPSIN expression.Scientific reports · 2024Article
- Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4.Molecular cell · 2024Article
- Article
- Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes.Nucleic acids research · 2024Article
- Antimicrobial and Anesthetic Niosomal Formulations Based on Amino Acid-Derived Surfactants.Molecules (Basel, Switzerland) · 2024Article
84 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 2 institutions in 2 countries.
Funding
Abstract
Allostery is well documented for proteins but less recognized for DNA-protein interactions. Here, we report that specific binding of a protein on DNA is substantially stabilized or destabilized by another protein bound nearby. The ternary complex's free energy oscillates as a function of the separation between the two proteins with a periodicity of ~10 base pairs, the helical pitch of B-form DNA, and a decay length of ~15 base pairs. The binding affinity of a protein near a DNA hairpin is similarly dependent on their separation, which-together with molecular dynamics simulations-suggests that deformation of the double-helical structure is the origin of DNA allostery. The physiological relevance of this phenomenon is illustrated by its effect on gene expression in live bacteria and on a transcription factor's affinity near nucleosomes.
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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.