ArticleNucleic acids research2018
Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 21 citations in OpenAlex.
- Integration host factor regulates antibiotic susceptibility through modulating alanine metabolism inFrontiers in microbiology · 2025Article
- Attenuated mutants ofExperimental biology and medicine (Maywood, N.J.) · 2024Article
- Mycobacterial IHF is a highly dynamic nucleoid-associated protein that assists HupB in organizing chromatin.Frontiers in microbiology · 2023Article
- Integration Host Factor Binds DNA Holliday Junctions.International journal of molecular sciences · 2022Article
- "Flexible hinge" dynamics in mismatched DNA revealed by fluorescence correlation spectroscopy.Journal of biological physics · 2022Article
- Reciprocally rewiring and repositioning the Integration Host Factor (IHF) subunit genes inMicrobial genomics · 2022Article
- Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF.Computational and structural biotechnology journal · 2022Article
- Sequence specificity, energetics and mechanism of mismatch recognition by DNA damage sensing protein Rad4/XPC.Nucleic acids research · 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
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate potential binding sites prior to recognition have remained elusive for most systems. Here we present these dynamics for Integration Host factor (IHF), a nucleoid-associated architectural protein, using a μs-resolved T-jump approach. Our studies show two distinct DNA-bending steps during site recognition by IHF. While the faster (∼100 μs) step is unaffected by changes in DNA or protein sequence that alter affinity by >100-fold, the slower (1-10 ms) step is accelerated ∼5-fold when mismatches are introduced at DNA sites that are sharply kinked in the specific complex. The amplitudes of the fast phase increase when the specific complex is destabilized and decrease with increasing [salt], which increases specificity. Taken together, these results indicate that the fast phase is non-specific DNA bending while the slow phase, which responds only to changes in DNA flexibility at the kink sites, is specific DNA kinking during site recognition. Notably, the timescales for the fast phase overlap with one-dimensional diffusion times measured for several proteins on DNA, suggesting that these dynamics reflect partial DNA bending during interrogation of potential binding sites by IHF as it scans DNA.
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