ArticleNucleic acids research2023
Single-molecule characterization of target search dynamics of DNA-binding proteins in DNA-condensed droplets.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 18 citations in OpenAlex.
- Acceleration of DNA reactions on the algae-based microrobots.Journal of nanobiotechnology · 2026Article
- Microprotein Regulates G-quadruplex Driven RNA Aggregation.bioRxiv : the preprint server for biology · 2026Article
- Nanoscale domains govern local diffusion and ageing within fused-in-sarcoma condensates.Nature nanotechnology · 2026Article
- Surface-Tethering Enhances Precision in Measuring Diffusion Within 3D Protein Condensates.Journal of molecular biology · 2026Article
- Compaction of chromatin domains regulates target search times of proteins.PLoS computational biology · 2026Article
- Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein.Nature communications · 2025Article
- Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein.bioRxiv : the preprint server for biology · 2025Article
- Surface-Tethering Enhances Precision in Measuring Diffusion Within 3D Protein Condensates.bioRxiv : the preprint server for biology · 2025Article
- RecN and RecA orchestrate an ordered DNA supercompaction response following ciprofloxacin-induced DNA damage in Escherichia coli.Nucleic acids research · 2025Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Target search models of DNA-binding proteins in cells typically consider search mechanisms that include 3D diffusion and 1D sliding, which can be characterized by single-molecule tracking on DNA. However, the finding of liquid droplets of DNA and nuclear components in cells cast doubt on extrapolation from the behavior in ideal non-condensed DNA conditions to those in cells. In this study, we investigate the target search behavior of DNA-binding proteins in reconstituted DNA-condensed droplets using single-molecule fluorescence microscopy. To mimic nuclear condensates, we reconstituted DNA-condensed droplets using dextran and PEG polymers. In the DNA-condensed droplets, we measured the translational movement of four DNA-binding proteins (p53, Nhp6A, Fis and Cas9) and p53 mutants possessing different structures, sizes, and oligomeric states. Our results demonstrate the presence of fast and slow mobility modes in DNA-condensed droplets for the four DNA-binding proteins. The slow mobility mode capability is correlated strongly to the molecular size and the number of DNA-binding domains on DNA-binding proteins, but only moderately to the affinity to single DNA segments in non-condensed conditions. The slow mobility mode in DNA-condensed droplets is interpreted as a multivalent interaction mode of the DNA-binding protein to multiple DNA segments.
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