ArticleNucleic acids research2019
Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 20 citations in OpenAlex.
- LOOP-TAG: massively-parallel measurement of length-dependent protein-mediated DNA looping probabilities by tagmentationbioRxiv : the preprint server for biology · 2026Article
- Modular Scaffold Crystals for Programmable Installation and Structural Observation of DNA-Binding Proteins.bioRxiv : the preprint server for biology · 2026Article
- Mechanisms of DNA Damage Recognition by UDG and PARP1 in the Nucleosome.Biomolecules · 2025Article
- Interferometric excitation fluorescence lifetime imaging microscopy.Nature communications · 2024Article
- Extensive Bioinformatics Analyses Reveal a Phylogenetically Conserved Winged Helix (WH) Domain (Zτ) of Topoisomerase IIα, Elucidating Its Very High Affinity for Left-Handed Z-DNA and Suggesting Novel Putative Functions.International journal of molecular sciences · 2023Article
- Molecular contacts in the Cren7-DNA complex: A quantitative investigation for electrostatic interaction.Biophysical journal · 2023Article
- Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM.Nucleic acids research · 2022Article
- Single-Molecule Methods for Investigating the Double-Stranded DNA Bendability.Molecules and cells · 2022Review
- Designed architectural proteins that tune DNA looping in bacteria.Nucleic acids research · 2021Article
- The role of FACT in managing chromatin: disruption, assembly, or repair?Nucleic acids research · 2020Review
- The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA.Nucleic acids research · 2020Article
- Sequence specificity, energetics and mechanism of mismatch recognition by DNA damage sensing protein Rad4/XPC.Nucleic acids research · 2020Article
- Review
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The yeast Nhp6A protein (yNhp6A) is a member of the eukaryotic HMGB family of chromatin factors that enhance apparent DNA flexibility. yNhp6A binds DNA nonspecifically with nM affinity, sharply bending DNA by >60°. It is not known whether the protein binds to unbent DNA and then deforms it, or if bent DNA conformations are 'captured' by protein binding. The former mechanism would be supported by discovery of conditions where unbent DNA is bound by yNhp6A. Here, we employed an array of conformational probes (FRET, fluorescence anisotropy, and circular dichroism) to reveal solution conditions in which an 18-base-pair DNA oligomer indeed remains bound to yNhp6A while unbent. In 100 mM NaCl, yNhp6A-bound DNA unbends as the temperature is raised, with no significant dissociation of the complex detected up to ∼45°C. In 200 mM NaCl, DNA unbending in the intact yNhp6A complex is again detected up to ∼35°C. Microseconds-resolved laser temperature-jump perturbation of the yNhp6a-DNA complex revealed relaxation kinetics that yielded unimolecular DNA bending/unbending rates on timescales of 500 μs-1 ms. These data provide the first direct observation of bending/unbending dynamics of DNA in complex with yNhp6A, suggesting a bind-then-bend mechanism for this protein.
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