ArticleMolecular cell2021
Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins.
Article in Molecular cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed, 87 citations in OpenAlex.
- Fast assembly and in vivo coalescence of ParBF biocondensates involved in bacterial DNA partition.Nucleic acids research · 2026Article
- Plasmid-encoded host reprogramming promotes plasmid dissemination.bioRxiv : the preprint server for biology · 2026Article
- Bipartite DNA binding domain of transcription factor BCL11B binds clustered short DNA sequence motifs.bioRxiv : the preprint server for biology · 2026Article
- Structural and functional implications of phase separation of membrane protein LacY in Escherichia coli.Nature communications · 2026Article
- Compaction of chromatin domains regulates target search times of proteins.PLoS computational biology · 2026Article
- Genome-wide DNA bridging by H-NS reshapes the stationary phase nucleoid and transcriptional landscape.bioRxiv : the preprint server for biology · 2025Article
- Article
- The Escherichia coli replication initiator DnaA is titrated on the chromosome.Nature communications · 2025Article
- Pointwise prediction of protein diffusive properties using machine learning.JPhys photonics · 2025Article
- In vivo single-molecule imaging of RecB reveals efficient repair of DNA damage in Escherichia coli.Nucleic acids research · 2025Article
- RecN and RecA orchestrate an ordered DNA supercompaction response following ciprofloxacin-induced DNA damage in Escherichia coli.Nucleic acids research · 2025Article
- Two transmembrane transcriptional regulators coordinate to activate chitin-induced natural transformation in Vibrio cholerae.PLoS genetics · 2025Article
- Relative Distribution of DnaA and DNA inInternational journal of molecular sciences · 2025Article
- Memory effects of transcription regulator-DNA interactions in bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Dynamics in Cre-loxP site-specific recombination.Current opinion in structural biology · 2024Review
- Article
- Robust Quantification of Live-Cell Single-Molecule Tracking Data for Fluorophores with Different Photophysical Properties.The journal of physical chemistry. B · 2024Article
- Stress-induced nucleoid remodeling in Deinococcus radiodurans is associated with major changes in Heat Unstable (HU) protein dynamics.Nucleic acids research · 2024Article
- A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery.eLife · 2024Article
- Live-cell imaging reveals the trade-off between target search flexibility and efficiency for Cas9 and Cas12a.Nucleic acids research · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
Abstract
Despite their diverse biochemical characteristics and functions, all DNA-binding proteins share the ability to accurately locate their target sites among the vast excess of non-target DNA. Toward identifying universal mechanisms of the target search, we used single-molecule tracking of 11 diverse DNA-binding proteins in living Escherichia coli. The mobility of these proteins during the target search was dictated by DNA interactions rather than by their molecular weights. By generating cells devoid of all chromosomal DNA, we discovered that the nucleoid is not a physical barrier for protein diffusion but significantly slows the motion of DNA-binding proteins through frequent short-lived DNA interactions. The representative DNA-binding proteins (irrespective of their size, concentration, or function) spend the majority (58%-99%) of their search time bound to DNA and occupy as much as ∼30% of the chromosomal DNA at any time. Chromosome crowding likely has important implications for the function of all DNA-binding proteins.
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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.