ArticleJournal of molecular biology2018
High Free-Energy Barrier of 1D Diffusion Along DNA by Architectural DNA-Binding Proteins.
Article in Journal of molecular biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 39 citations in OpenAlex.
- Single-molecule imaging reveals DNA shape read-out by the INO80 chromatin remodeler.Nature communications · 2026Article
- Single-trajectory Bayesian modeling reveals multi-state diffusion of the MSH sliding clamp.NPJ systems biology and applications · 2026Article
- Article
- How to scan naked DNA using promiscuous recognition and no clamping: a model for pioneer transcription factors.Nucleic acids research · 2024Article
- Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes.Nucleic acids research · 2024Article
- Single-molecule characterization of target search dynamics of DNA-binding proteins in DNA-condensed droplets.Nucleic acids research · 2023Article
- Rational design of phase separating peptides based on phase separating protein sequence of p53.Scientific reports · 2023Article
- Locally correlated kinetics of post-replication DNA methylation reveals processivity and region specificity in DNA methylation maintenance.Journal of the Royal Society, Interface · 2022Article
- Apparent anomalous diffusion and non-Gaussian distributions in a simple mobile-immobile transport model with Poissonian switching.Journal of the Royal Society, Interface · 2022Article
- Structure-dependent recruitment and diffusion of guest proteins in liquid droplets of FUS.Scientific reports · 2022Article
- Molecular principles of recruitment and dynamics of guest proteins in liquid droplets.Scientific reports · 2021Article
- Direct visualization of the effect of DNA structure and ionic conditions on HU-DNA interactions.Scientific reports · 2021Article
- Engineering of the genome editing protein Cas9 to slide along DNA.Scientific reports · 2021Article
- The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA.Nucleic acids research · 2020Article
- Nucleosome allostery in pioneer transcription factor binding.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Transient binding and jumping dynamics of p53 along DNA revealed by sub-millisecond resolved single-molecule fluorescence tracking.Scientific reports · 2020Article
- How p53 Molecules Solve the Target DNA Search Problem: A Review.International journal of molecular sciences · 2020Review
- Rational design using sequence information only produces a peptide that binds to the intrinsically disordered region of p53.Scientific reports · 2019Article
- Quantifying the two-state facilitated diffusion model of protein-DNA interactions.Nucleic acids research · 2019Article
- Sliding Mechanism at a Coiled-Coil Interface.Biophysical journal · 2019Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Architectural DNA-binding proteins function to regulate diverse DNA reactions and have the defining property of significantly changing DNA conformation. Although the 1D movement along DNA by other types of DNA-binding proteins has been visualized, the mobility of architectural DNA-binding proteins on DNA remains unknown. Here, we applied single-molecule fluorescence imaging on arrays of extended DNA molecules to probe the binding dynamics of three structurally distinct architectural DNA-binding proteins: Nhp6A, HU, and Fis. Each of these proteins was observed to move along DNA, and the salt concentration independence of the 1D diffusion implies sliding with continuous contact to DNA. Nhp6A and HU exhibit a single sliding mode, whereas Fis exhibits two sliding modes. Based on comparison of the diffusion coefficients and sizes of many DNA binding proteins, the architectural proteins are categorized into a new group distinguished by an unusually high free-energy barrier for 1D diffusion. The higher free-energy barrier for 1D diffusion by architectural proteins can be attributed to the large DNA conformational changes that accompany binding and impede rotation-coupled movement along the DNA grooves.
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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.