ArticleBiophysical journal2017
DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid.
Article in Biophysical journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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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Who cites it
10 citing papers in PubMed, 25 citations in OpenAlex.
- Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in liveProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in livebioRxiv : the preprint server for biology · 2024Article
- Probing Amyloid-DNA Interaction with Nanofluidics.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Local rigidification and possible coacervation of the Escherichia coli DNA by cationic nylon-3 polymers.Biophysical journal · 2021Article
- Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins.Molecular cell · 2021Article
- Article
- Diffusion of DNA-Binding Species in the Nucleus: A Transient Anomalous Subdiffusion Model.Biophysical journal · 2020Article
- Rigidification of theProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Understanding Protein Mobility in Bacteria by Tracking Single Molecules.Journal of molecular biology · 2018Review
- How Important Is Protein Diffusion in Prokaryotes?Frontiers in molecular biosciences · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors must diffuse through densely packed and coiled DNA to find their binding sites. Using a coarse-grained model of DNA and lac repressor (LacI) in the Escherichia coli nucleoid, simulations were performed to examine how LacI diffuses in such a space. Despite the canonical picture of LacI diffusing rather freely, in reality the DNA is densely packed, is not rigid but highly mobile, and the dynamics of DNA dictates to a great extent the LacI motion. A possibly better picture of unbound LacI motion is that of gated diffusion, where DNA confines LacI in a cage, but LacI can move between cages when hindering DNA strands move out of the way. Three-dimensional diffusion constants for unbound LacI computed from simulations closely match those for unbound LacI in vivo reported in the literature. The internal motions of DNA appear to be governed by strong internal forces arising from being crowded into the small space of the nucleoid. A consequence of the DNA internal motion is that protein target search may be accelerated.
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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.