ArticleNucleic acids research2013
Control of DNA minor groove width and Fis protein binding by the purine 2-amino group.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed, 88 citations in OpenAlex.
- Cepharanthine as a potential Fis inhibitor enhances Enrofloxacin efficacy against Pasteurella multocida.BMC microbiology · 2026Article
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- DNAdesign: feature-aware in silico design of synthetic DNA through mutation.Bioinformatics (Oxford, England) · 2025Article
- SynonymousNAR genomics and bioinformatics · 2024Article
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- Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation.Nucleic acids research · 2024Article
- Dissection of integrated readout reveals the structural thermodynamics of DNA selection by transcription factors.Structure (London, England : 1993) · 2024Article
- Substrate DNA Promoting Binding ofMicroorganisms · 2023Article
- Noncanonical binding of transcription factors: time to revisitMolecular biology of the cell · 2023Review
- Synthesis and photophysical characterization of fluorescent indole nucleoside analogues.RSC advances · 2023Article
- Energy Landscapes for Base-Flipping in a Model DNA Duplex.The journal of physical chemistry. B · 2022Article
- Facilitated dissociation of nucleoid-associated proteins from DNA in the bacterial confinement.Biophysical journal · 2022Article
- Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation.International journal of molecular sciences · 2020Article
- Fis Contributes to Resistance of Pseudomonas aeruginosa to Ciprofloxacin by Regulating Pyocin Synthesis.Journal of bacteriology · 2020Article
- Crystal structure of the nucleoid-associated protein Fis (PA4853) from Pseudomonas aeruginosa.Acta crystallographica. Section F, Structural biology communications · 2020Article
- Article
- New protein-DNA complexes in archaea: a small monomeric protein induces a sharp V-turn DNA structure.Scientific reports · 2019Article
- Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR.Nucleic acids research · 2019Article
- Cooperative DNA binding by proteins through DNA shape complementarity.Nucleic acids research · 2019Article
- Energy Transfer as A Driving Force in Nucleic Acid⁻Protein Interactions.Molecules (Basel, Switzerland) · 2019Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The width of the DNA minor groove varies with sequence and can be a major determinant of DNA shape recognition by proteins. For example, the minor groove within the center of the Fis-DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto the protein surface. G/C base pairs within this segment, which is not contacted by the Fis protein, reduce binding affinities up to 2000-fold over A/T-rich sequences. We show here through multiple X-ray structures and binding properties of Fis-DNA complexes containing base analogs that the 2-amino group on guanine is the primary molecular determinant controlling minor groove widths. Molecular dynamics simulations of free-DNA targets with canonical and modified bases further demonstrate that sequence-dependent narrowing of minor groove widths is modulated almost entirely by the presence of purine 2-amino groups. We also provide evidence that protein-mediated phosphate neutralization facilitates minor groove compression and is particularly important for binding to non-optimally shaped DNA duplexes.
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