ArticleNucleic acids research2008
What drives the binding of minor groove-directed ligands to DNA hairpins?
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Conditional Cooperativity in DNA Minor-Groove Recognition by Oligopeptides.Molecules (Basel, Switzerland) · 2021Article
- Differential scanning calorimetric study of antibiotic distamycin A binding with chromatin within isolated rat liver nuclei.Pharmaceutical biology · 2017Article
- Anomalous Separation of Small Y-Chromosomal DNA Fragments on Microchip Electrophoresis.Scientia pharmaceutica · 2016Article
- Thermodynamic fingerprints of ligand binding to human telomeric G-quadruplexes.Nucleic acids research · 2015Article
- Dominant Driving Forces in Human Telomere Quadruplex Binding-Induced Structural Alterations.Biophysical journal · 2015Article
- Differentiation and distributions of DNA/cisplatin crosslinks by liquid chromatography-electrospray ionization-infrared multiphoton dissociation mass spectrometry.Journal of the American Society for Mass Spectrometry · 2014Article
- Study on the binding interaction between perfluoroalkyl acids and DNA.Environmental science and pollution research international · 2013Article
- Complexity in the binding of minor groove agents: netropsin has two thermodynamically different DNA binding modes at a single site.Nucleic acids research · 2011Article
- Influence of a hairpin loop on the thermodynamic stability of a DNA oligomer.Journal of nucleic acids · 2011Article
- DNA duplex stability: the role of preorganized electrostatics.The journal of physical chemistry. B · 2010Article
- Driving forces of gyrase recognition by the addiction toxin CcdB.The Journal of biological chemistry · 2009Article
- Binding of PFOS to serum albumin and DNA: insight into the molecular toxicity of perfluorochemicals.BMC molecular biology · 2009Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the molecular basis of ligand-DNA-binding events, and its application to the rational design of novel drugs, requires knowledge of the structural features and forces that drive the corresponding recognition processes. Existing structural evidence on DNA complexation with classical minor groove-directed ligands and the corresponding studies of binding energetics have suggested that this type of binding can be described as a rigid-body association. In contrast, we show here that the binding-coupled conformational changes may be crucial for the interpretation of DNA (hairpin) association with a classical minor groove binder (netropsin). We found that, although the hairpin form is the only accessible state of ligand-free DNA, its association with the ligand may lead to its transition into a duplex conformation. It appears that formation of the fully ligated duplex from the ligand-free hairpin, occurring via two pathways, is enthalpically driven and accompanied by a significant contribution of the hydrophobic effect. Our thermodynamic and structure-based analysis, together with corresponding theoretical studies, shows that none of the predicted binding steps can be considered as a rigid-body association. In this light we anticipate our thermodynamic approach to be the basis of more sophisticated nucleic acid recognition mechanisms, which take into account the dynamic nature of both the nucleic acid and the ligand molecule.
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