ArticleJournal of molecular biology2008
Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 36 citations in OpenAlex.
- DNA deformability in sequence-dependent capture of E. coli gyrase.Nature communications · 2026Article
- Contributions of Local Structural and Energetic Features of DNA to Large-scale Genomic Organization.Journal of molecular biology · 2026Review
- emDNA - A Tool for Modeling Protein-decorated DNA Loops and Minicircles at the Base-pair Step Level.Journal of molecular biology · 2022Article
- Effect of DNA Flexibility on Complex Formation of a Cationic Nanoparticle with Double-Stranded DNA.ACS omega · 2021Article
- Insights into Genome Architecture Deduced from the Properties of Short Lac Repressor-mediated DNA Loops.Biophysical reviews · 2016Article
- High-resolution mapping of architectural DNA binding protein facilitation of a DNA repression loop in Escherichia coli.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- DNA topology confers sequence specificity to nonspecific architectural proteins.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- What controls DNA looping?International journal of molecular sciences · 2014Article
- Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Quantitative influence of macromolecular crowding on gene regulation kinetics.Nucleic acids research · 2014Article
- DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation.Physical biology · 2013Article
- Analyzing and building nucleic acid structures with 3DNA.Journal of visualized experiments : JoVE · 2013Article
- A model of H-NS mediated compaction of bacterial DNA.Biophysical journal · 2013Article
- Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations.Biochemical Society transactions · 2013Review
- Article
- Insights into Gene Expression and Packaging from Computer Simulations.Biophysical reviews · 2012Article
- Internucleosomal interactions mediated by histone tails allow distant communication in chromatin.The Journal of biological chemistry · 2012Article
- Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms.Journal of chemical theory and computation · 2012Article
- Understanding apparent DNA flexibility enhancement by HU and HMGB architectural proteins.Journal of molecular biology · 2011Article
- HU protein induces incoherent DNA persistence length.Biophysical journal · 2011Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The histone-like HU (heat unstable) protein plays a key role in the organization and regulation of the Escherichia coli genome. The nonspecific nature of HU binding to DNA complicates analysis of the mechanism by which the protein contributes to the looping of DNA. Conventional models of the looping of HU-bound duplexes attribute the changes in biophysical properties of DNA brought about by the random binding of protein to changes in the effective parameters of an ideal helical wormlike chain. Here, we introduce a novel Monte Carlo approach to study the effects of nonspecific HU binding on the configurational properties of DNA directly. We randomly decorated segments of an ideal double-helical DNA with HU molecules that induce the bends and other structural distortions of the double helix find in currently available X-ray structures. We find that the presence of HU at levels approximating those found in the cell reduces the persistence length by roughly threefold compared with that of naked DNA. The binding of protein has particularly striking effects on the cyclization properties of short duplexes, altering the dependence of ring closure on chain length in a way that cannot be mimicked by a simple wormlike model and accumulating at higher-than-expected levels on successfully closed chains. Moreover, the uptake of protein on small minicircles depends on chain length, taking advantage of the HU-induced deformations of DNA structure to facilitate ligation. Circular duplexes with bound HU show much greater propensity than protein-free DNA to exist as negatively supercoiled topoisomers, suggesting a potential role of HU in organizing the bacterial nucleoid. The local bending and undertwisting of DNA by HU, in combination with the number of bound proteins, provide a structural rationale for the condensation of DNA and the observed expression levels of reporter genes in vivo.
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