ArticleBiophysical journal2015
Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Strong field gradients enable NMR-based diffusion measurements for KJournal of magnetic resonance (San Diego, Calif. : 1997) · 2025Article
- Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA.Biochimica et biophysica acta. Gene regulatory mechanisms · 2025Review
- Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins.Nucleic acids research · 2023Article
- Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding.Nucleic acids research · 2023Article
- Dynamics of Cations around DNA and Protein as Revealed byAnalytical chemistry · 2022Article
- Hindered Rotations of Protein Asparagine/Glutamine Side-Chain NHThe journal of physical chemistry letters · 2021Article
- Dynamic Autoinhibition of the HMGB1 Protein via Electrostatic Fuzzy Interactions of Intrinsically Disordered Regions.Journal of molecular biology · 2021Article
- De novo determination of near-surface electrostatic potentials by NMR.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Quantifying and visualizing weak interactions between anions and proteins.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Circular and linear: a tale of aptamer selection for the activation of SIRT1 to induce death in cancer cells.RSC advances · 2020Article
- Dynamics of Ionic Interactions at Protein-Nucleic Acid Interfaces.Accounts of chemical research · 2020Article
- An artificial cationic oligosaccharide combined with phosphorothioate linkages strongly improves siRNA stability.Scientific reports · 2020Article
- Racemic phosphorothioate as a tool for NMR investigations of protein-DNA complexes.Journal of biomolecular NMR · 2020Article
- Enhanced affinity of racemic phosphorothioate DNA with transcription factor SATB1 arising from diastereomer-specific hydrogen bonds and hydrophobic contacts.Nucleic acids research · 2020Article
- Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL.Nature communications · 2020Article
- NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups.The journal of physical chemistry. B · 2020Article
- Detecting Counterion Dynamics in DNA-Protein Association.Angewandte Chemie (International ed. in English) · 2020Article
- Mobility of Histidine Side Chains Analyzed withThe journal of physical chemistry. B · 2019Article
- NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics.Methods in enzymology · 2019Review
- NMR-based investigations into target DNA search processes of proteins.Methods (San Diego, Calif.) · 2018Review
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6 authors.
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Abstract
Dithioation of DNA phosphate is known to enhance binding affinities, at least for some proteins. We mechanistically characterized this phenomenon for the Antennapedia homeodomain-DNA complex by integrated use of fluorescence, isothermal titration calorimetry, NMR spectroscopy, and x-ray crystallography. By fluorescence and isothermal titration calorimetry, we found that this affinity enhancement is entropy driven. By NMR, we investigated the ionic hydrogen bonds and internal motions of lysine side-chain NH3(+) groups involved in ion pairs with DNA. By x-ray crystallography, we compared the structures of the complexes with and without dithioation of the phosphate. Our NMR and x-ray data show that the lysine side chain in contact with the DNA phosphate becomes more dynamic upon dithioation. Our thermodynamic, structural, and dynamic investigations collectively suggest that the affinity enhancement by the oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic gain arising from mobilization of the intermolecular ion pair at the protein-DNA interface.
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