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Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
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Conformational dynamics of an ATP-binding DNA aptamer: a single-molecule study
Tie Xia1, Jinghe Yuan, Xiaohong Fang
1Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructure and Nanotechnology, Chinese Academy of Sciences , Beijing 100190, P. R. China.
The Journal of Physical Chemistry. B
|November 20, 2013
Summary
This study reveals DNA aptamers recognize ATP through conformational selection. The aptamer pre-exists in a folded state, and ATP binding stabilizes this structure, supporting the conformational selection mechanism in molecular recognition.
Area of Science:
- Molecular Biology
- Biochemistry
- Biophysics
Background:
- Nucleic acid aptamers are DNA or RNA molecules with high target specificity.
- The mechanism of aptamer-target recognition (induced fit vs. conformational selection) remains debated.
- Understanding this mechanism is crucial for aptamer-based biomedical applications.
Purpose of the Study:
- To investigate the conformational dynamics of an ATP-binding DNA aptamer.
- To determine whether the aptamer utilizes induced fit or conformational selection for ATP binding.
- To elucidate the molecular recognition mechanism of aptamers.
Main Methods:
- Selection of an ATP-binding DNA aptamer as a model system.
- Utilized single-pair Förster resonance energy transfer (spFRET) spectroscopy.
- Analyzed aptamer conformational properties with and without ATP.
Main Results:
- The aptamer adopts a double-stranded-like, folded conformation even without ATP.
- This folded state is conformationally dynamic, especially at low salt concentrations.
- ATP binding stabilizes the folded conformation, shifting the equilibrium towards the ligand-bound state.
Conclusions:
- The ATP-binding DNA aptamer employs conformational selection for ATP recognition.
- The aptamer exists in an equilibrium of conformations, with ATP stabilizing the functional state.
- This finding clarifies a fundamental aspect of aptamer-target interactions.
