ArticleNucleic acids research2014
Search by proteins for their DNA target site: 1. The effect of DNA conformation on protein sliding.
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 22 papers.
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Who cites it
22 citing papers in PubMed, 59 citations in OpenAlex.
- Cryo-EM structure of a 95-base-pair double-stranded DNA minicircle at 5.3 Å resolution.Nucleic acids research · 2026Article
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- Modeling Facilitated Diffusion of Proteins in Crowded Environment.Sub-cellular biochemistry · 2025Review
- Article
- Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes.Nucleic acids research · 2024Article
- Interdomain dynamics in human Replication Protein A regulates kinetics and thermodynamics of its binding to ssDNA.PloS one · 2023Article
- Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA.Biophysical journal · 2022Article
- Understanding protein diffusion on force-induced stretched DNA conformation.Frontiers in molecular biosciences · 2022Article
- Direct visualization of the effect of DNA structure and ionic conditions on HU-DNA interactions.Scientific reports · 2021Article
- What Are the Molecular Requirements for Protein Sliding along DNA?The journal of physical chemistry. B · 2021Article
- Prerecognition Diffusion Mechanism of Human DNA Mismatch Repair Proteins along DNA: Msh2-Msh3 versus Msh2-Msh6.Biochemistry · 2020Article
- Nucleosome allostery in pioneer transcription factor binding.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Differential Scaling of Gene Expression with Cell Size May Explain Size Control in Budding Yeast.Molecular cell · 2020Article
- Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu.Biophysical journal · 2020Article
- Quantifying the two-state facilitated diffusion model of protein-DNA interactions.Nucleic acids research · 2019Article
- Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins.Scientific reports · 2018Article
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- Impacts of the charged residues mutation S48E/N62H on the thermostability and unfolding behavior of cold shock protein: insights from molecular dynamics simulation with Gō model.Journal of molecular modeling · 2016Article
- A human transcription factor in search mode.Nucleic acids research · 2016Article
- Searching target sites on DNA by proteins: Role of DNA dynamics under confinement.Nucleic acids research · 2015Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recognition of DNA-binding proteins (DBPs) to their specific site often precedes by a search technique in which proteins slide, hop along the DNA contour or perform inter-segment transfer and 3D diffusion to dissociate and re-associate to distant DNA sites. In this study, we demonstrated that the strength and nature of the non-specific electrostatic interactions, which govern the search dynamics of DBPs, are strongly correlated with the conformation of the DNA. We tuned two structural parameters, namely curvature and the extent of helical twisting in circular DNA. These two factors are mutually independent of each other and can modulate the electrostatic potential through changing the geometry of the circular DNA conformation. The search dynamics for DBPs on circular DNA is therefore markedly different compared with linear B-DNA. Our results suggest that, for a given DBP, the rotation-coupled sliding dynamics is precluded in highly curved DNA (as well as for over-twisted DNA) because of the large electrostatic energy barrier between the inside and outside of the DNA molecule. Under such circumstances, proteins prefer to hop in order to explore interior DNA sites. The change in the balance between sliding and hopping propensities as a function of DNA curvature or twisting may result in different search efficiency and speed.
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