Thermodynamic analysis of cooperative ligand binding by the ATP-binding DNA aptamer indicates a population-shift binding mechanism
| Autor: | Sladjana Slavkovic, Anne E. Johnson, Yanrui Zhu, Philip E. Johnson, Aron A. Shoara, Zachary R. Churcher |
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| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Magnetic Resonance Spectroscopy Base pair Aptamer lcsh:Medicine Cooperativity Calorimetry 010402 general chemistry 01 natural sciences Article 03 medical and health sciences chemistry.chemical_compound Adenosine Triphosphate Biophysical chemistry Binding site lcsh:Science Binding Sites Multidisciplinary lcsh:R Cooperative binding Bioanalytical chemistry Isothermal titration calorimetry DNA Aptamers Nucleotide Ligand (biochemistry) 0104 chemical sciences 030104 developmental biology chemistry Biophysics Thermodynamics lcsh:Q |
| Zdroj: | Scientific Reports, Vol 10, Iss 1, Pp 1-10 (2020) Scientific Reports |
| ISSN: | 2045-2322 |
| DOI: | 10.1038/s41598-020-76002-8 |
| Popis: | The ATP-binding DNA aptamer is often used as a model system for developing new aptamer-based biosensor methods. This aptamer follows a structure-switching binding mechanism and is unusual in that it binds two copies of its ligand. We have used isothermal titration calorimetry methods to study the binding of ATP, ADP, AMP and adenosine to the ATP-binding aptamer. Using both individual and global fitting methods, we show that this aptamer follows a positive cooperative binding mechanism. We have determined the binding affinity and thermodynamics for both ligand-binding sites. By separating the ligand-binding sites by an additional four base pairs, we engineered a variant of this aptamer that binds two adenosine ligands in an independent manner. Together with NMR and thermal stability experiments, these data indicate that the ATP-binding DNA aptamer follows a population-shift binding mechanism that is the source of the positive binding cooperativity by the aptamer. |
| Databáze: | OpenAIRE |
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