ArticleJournal of molecular biology2011
Understanding apparent DNA flexibility enhancement by HU and HMGB architectural proteins.
Article in Journal of molecular biology, 2011. 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, 39 citations in OpenAlex.
- LOOP-TAG: massively-parallel measurement of length-dependent protein-mediated DNA looping probabilities by tagmentationbioRxiv : the preprint server for biology · 2026Article
- High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics.Biophysical journal · 2022Article
- Designed architectural proteins that tune DNA looping in bacteria.Nucleic acids research · 2021Article
- Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling.Nature communications · 2020Article
- Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A.Nucleic acids research · 2019Article
- Static Kinks or Flexible Hinges: Multiple Conformations of Bent DNA Bound to Integration Host Factor Revealed by Fluorescence Lifetime Measurements.The journal of physical chemistry. B · 2018Article
- High Free-Energy Barrier of 1D Diffusion Along DNA by Architectural DNA-Binding Proteins.Journal of molecular biology · 2018Article
- Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-κB inhibition activity.Nucleic acids research · 2017Article
- Insights into Genome Architecture Deduced from the Properties of Short Lac Repressor-mediated DNA Loops.Biophysical reviews · 2016Article
- The HMGB1 C-Terminal Tail Regulates DNA Bending.Journal of molecular biology · 2016Article
- HU multimerization shift controls nucleoid compaction.Science advances · 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
- Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins.Biochemistry · 2014Article
- Analyzing and building nucleic acid structures with 3DNA.Journal of visualized experiments : JoVE · 2013Article
- Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations.Biochemical Society transactions · 2013Review
- Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility.Nucleic acids research · 2013Article
- Article
- Single-molecule FRET analysis of DNA binding and bending by yeast HMGB protein Nhp6A.Nucleic acids research · 2013Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Understanding and predicting the mechanical properties of protein/DNA complexes are challenging problems in biophysics. Certain architectural proteins bind DNA without sequence specificity and strongly distort the double helix. These proteins rapidly bind and unbind, seemingly enhancing the flexibility of DNA as measured by cyclization kinetics. The ability of architectural proteins to overcome DNA stiffness has important biological consequences, but the detailed mechanism of apparent DNA flexibility enhancement by these proteins has not been clear. Here, we apply a novel Monte Carlo approach that incorporates the precise effects of protein on DNA structure to interpret new experimental data for the bacterial histone-like HU protein and two eukaryotic high-mobility group class B (HMGB) proteins binding to ∼200-bp DNA molecules. These data (experimental measurement of protein-induced increase in DNA cyclization) are compared with simulated cyclization propensities to deduce the global structure and binding characteristics of the closed protein/DNA assemblies. The simulations account for all observed (chain length and concentration dependent) effects of protein on DNA behavior, including how the experimental cyclization maxima, observed at DNA lengths that are not an integral helical repeat, reflect the deformation of DNA by the architectural proteins and how random DNA binding by different proteins enhances DNA cyclization to different levels. This combination of experiment and simulation provides a powerful new approach to resolve a long-standing problem in the biophysics of protein/DNA interactions.
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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.