ArticleProceedings of the National Academy of Sciences of the United States of America2014
DNA topology confers sequence specificity to nonspecific architectural proteins.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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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
26 citing papers in PubMed, 41 citations in OpenAlex.
- Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.Current opinion in structural biology · 2026Review
- Molecular insights into the fine-tuning of pH-dependent ArsR-mediated regulation of the SabA adhesin in Helicobacter pylori.Nucleic acids research · 2024Article
- Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments.Nucleic acids research · 2024Article
- Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization-A Timing Chain for the Bacterial Growth Cycle?Biomolecules · 2022Review
- emDNA - A Tool for Modeling Protein-decorated DNA Loops and Minicircles at the Base-pair Step Level.Journal of molecular biology · 2022Article
- Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF.Computational and structural biotechnology journal · 2022Article
- Supercoiling and looping promote DNA base accessibility and coordination among distant sites.Nature communications · 2021Article
- Synergy between Protein Positioning and DNA Elasticity: Energy Minimization of Protein-Decorated DNA Minicircles.The journal of physical chemistry. B · 2021Article
- Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling.Nature communications · 2020Article
- Biophysical Reviews' "Meet the Editors Series"-a profile of Wilma K. Olson.Biophysical reviews · 2020Article
- Ciprofloxacin impairs mitochondrial DNA replication initiation through inhibition of Topoisomerase 2.Nucleic acids research · 2018Article
- Chromosomal organization of transcription: in a nutshell.Current genetics · 2018Review
- Novel insights into chromosomal conformations in cancer.Molecular cancer · 2017Review
- HU content and dynamics in Escherichia coli during the cell cycle and at different growth rates.FEMS microbiology letters · 2017Article
- Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.Nucleic acids research · 2017Article
- Influence of DNA sequence on the structure of minicircles under torsional stress.Nucleic acids research · 2017Article
- Novel clades of the HU/IHF superfamily point to unexpected roles in the eukaryotic centrosome, chromosome partitioning, and biologic conflicts.Cell cycle (Georgetown, Tex.) · 2017Article
- Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling.Biophysical journal · 2017Article
- Contributions of Sequence to the Higher-Order Structures of DNA.Biophysical journal · 2017Review
- Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation.Nucleic acids research · 2016Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Topological constraints placed on short fragments of DNA change the disorder found in chain molecules randomly decorated by nonspecific, architectural proteins into tightly organized 3D structures. The bacterial heat-unstable (HU) protein builds up, counter to expectations, in greater quantities and at particular sites along simulated DNA minicircles and loops. Moreover, the placement of HU along loops with the "wild-type" spacing found in the Escherichia coli lactose (lac) and galactose (gal) operons precludes access to key recognition elements on DNA. The HU protein introduces a unique spatial pathway in the DNA upon closure. The many ways in which the protein induces nearly the same closed circular configuration point to the statistical advantage of its nonspecificity. The rotational settings imposed on DNA by the repressor proteins, by contrast, introduce sequential specificity in HU placement, with the nonspecific protein accumulating at particular loci on the constrained duplex. Thus, an architectural protein with no discernible DNA sequence-recognizing features becomes site-specific and potentially assumes a functional role upon loop formation. The locations of HU on the closed DNA reflect long-range mechanical correlations. The protein responds to DNA shape and deformability—the stiff, naturally straight double-helical structure—rather than to the unique features of the constituent base pairs. The structures of the simulated loops suggest that HU architecture, like nucleosomal architecture, which modulates the ability of regulatory proteins to recognize their binding sites in the context of chromatin, may influence repressor-operator interactions in the context of the bacterial nucleoid.
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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.