ArticleNucleic acids research2014
Positive and negative impacts of nonspecific sites during target location by a sequence-specific DNA-binding protein: origin of the optimal search at physiological ionic strength.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Article
- Mechanisms for DNA Interplay in Eukaryotic Transcription Factors.Annual review of biophysics · 2025Review
- Analyzing paramagnetic NMR data on target DNA search by proteins using a discrete-state kinetic model for translocation.Biopolymers · 2024Article
- Dynamic interplay between target search and recognition for a Type I CRISPR-Cas system.Nature communications · 2023Article
- Diverse role of decoys on emergence and precision of oscillations in a biomolecular clock.Biophysical journal · 2021Article
- A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA.International journal of molecular sciences · 2021Article
- Nucleic acid binding by SAMHD1 contributes to the antiretroviral activity and is enhanced by the GpsN modification.Nature communications · 2021Article
- Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications.Biophysical chemistry · 2021Review
- Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates.Frontiers in molecular biosciences · 2021Review
- Article
- Racemic phosphorothioate as a tool for NMR investigations of protein-DNA complexes.Journal of biomolecular NMR · 2020Article
- Enhancement of gene expression noise from transcription factor binding to genomic decoy sites.Scientific reports · 2020Article
- Transcription Factor Binding in Embryonic Stem Cells Is Constrained by DNA Sequence Repeat Symmetry.Biophysical journal · 2020Article
- How p53 Molecules Solve the Target DNA Search Problem: A Review.International journal of molecular sciences · 2020Review
- Eukaryotic transcription factors can track and control their target genes using DNA antennas.Nature communications · 2020Article
- Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu.Biophysical journal · 2020Article
- Rational design of a DNA sequence-specific modular protein tag by tuning the alkylation kinetics.Chemical science · 2019Article
- Facilitated Diffusion Mechanisms in DNA Base Excision Repair and Transcriptional Activation.Chemical reviews · 2018Review
- DNA scanning by base excision repair enzymes and implications for pathway coordination.DNA repair · 2018Review
- NMR-based investigations into target DNA search processes of proteins.Methods (San Diego, Calif.) · 2018Review
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4 authors.
Funding
Abstract
The inducible transcription factor Egr-1, which recognizes a 9-bp target DNA sequence via three zinc-finger domains, rapidly activates particular genes upon cellular stimuli such as neuronal signals and vascular stresses. Here, using the stopped-flow fluorescence method, we measured the target search kinetics of the Egr-1 zinc-finger protein at various ionic strengths between 40 and 400 mM KCl and found the most efficient search at 150 mM KCl. We further investigated the kinetics of intersegment transfer, dissociation, and sliding of this protein on DNA at distinct concentrations of KCl. Our data suggest that Egr-1's kinetic properties are well suited for efficient scanning of chromosomal DNA in vivo. Based on a newly developed theory, we analyzed the origin of the optimal search efficiency at physiological ionic strength. Target association is accelerated by nonspecific binding to nearby sites and subsequent sliding to the target as well as by intersegment transfer. Although these effects are stronger at lower ionic strengths, such conditions also favor trapping of the protein at distant nonspecific sites, decelerating the target association. Our data demonstrate that Egr-1 achieves the optimal search at physiological ionic strength through a compromise between the positive and negative impacts of nonspecific interactions with DNA.
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