ArticleJournal of molecular biology2015
DNA-Segment-Facilitated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response.
Article in Journal of molecular biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 47 citations in OpenAlex.
- Compaction of chromatin domains regulates target search times of proteins.PLoS computational biology · 2026Article
- Single-molecule characterization of target search dynamics of DNA-binding proteins in DNA-condensed droplets.Nucleic acids research · 2023Article
- Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations.Nucleic acids research · 2022Article
- Facilitated dissociation of nucleoid-associated proteins from DNA in the bacterial confinement.Biophysical journal · 2022Article
- DNA-facilitated target search by nucleoproteins: Extension of a biosensor-surface plasmon resonance method.Analytical biochemistry · 2021Article
- Article
- 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
- The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA.Nucleic acids research · 2020Article
- How p53 Molecules Solve the Target DNA Search Problem: A Review.International journal of molecular sciences · 2020Review
- How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation.Current opinion in chemical biology · 2019Review
- Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds.Biophysical journal · 2019Article
- Damage sensor role of UV-DDB during base excision repair.Nature structural & molecular biology · 2019Article
- Mechanical unfolding of spectrin reveals a super-exponential dependence of unfolding rate on force.Scientific reports · 2019Article
- DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes.Nucleic acids research · 2019Article
- Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A.Nucleic acids research · 2019Article
- Polarized displacement by transcription activator-like effectors for regulatory circuits.Nature chemical biology · 2019Article
- Static Kinks or Flexible Hinges: Multiple Conformations of Bent DNA Bound to Integration Host Factor Revealed by Fluorescence Lifetime Measurements.The journal of physical chemistry. B · 2018Article
- DNA scanning by base excision repair enzymes and implications for pathway coordination.DNA repair · 2018Review
- Intrinsically disordered domain of tumor suppressor p53 facilitates target search by ultrafast transfer between different DNA strands.Nucleic acids research · 2018Article
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Authors and funding
8 authors at 4 institutions in 1 country.
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Abstract
The rate of dissociation of a DNA-protein complex is often considered to be a property of that complex, without dependence on other nearby molecules in solution. We study the kinetics of dissociation of the abundant Escherichia coli nucleoid protein Fis from DNA, using a single-molecule mechanics assay. The rate of Fis dissociation from DNA is strongly dependent on the solution concentration of DNA. The off-rate (k(off)) of Fis from DNA shows an initially linear dependence on solution DNA concentration, characterized by an exchange rate of k(ex)≈9×10(-4) (ng/μl)(-1) s(-1) for 100 mM univalent salt buffer, with a very small off-rate at zero DNA concentration. The off-rate saturates at approximately k(off,max)≈8×10(-3) s(-1) for DNA concentrations above ≈20 ng/μl. This exchange reaction depends mainly on DNA concentration with little dependence on the length of the DNA molecules in solution or on binding affinity, but this does increase with increasing salt concentration. We also show data for the yeast HMGB protein NHP6A showing a similar DNA-concentration-dependent dissociation effect, with faster rates suggesting generally weaker DNA binding by NHP6A relative to Fis. Our results are well described by a model with an intermediate partially dissociated state where the protein is susceptible to being captured by a second DNA segment, in the manner of "direct transfer" reactions studied for other DNA-binding proteins. This type of dissociation pathway may be important to protein-DNA binding kinetics in vivo where DNA concentrations are large.
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