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Ligand-Induced Folding in a Dopamine-Binding DNA Aptamer
Yunus A Kaiyum1, Emily Hoi Pui Chao1, Lakshmi Dhar1
1Department of Chemistry, York University, 4700 Keele St., Toronto, Ontario, M3 J 1P3, Canada.
Chembiochem : a European Journal of Chemical Biology
|October 6, 2024
Summary
DNA aptamers are key for biosensors, but their ligand-induced binding is unclear. This study reveals how dopamine aptamer structure changes upon binding, impacting biosensor function.
Area of Science:
- Biochemistry
- Molecular Biology
- Biophysics
Background:
- Aptamers are crucial molecular recognition elements in biosensor development.
- Ligand-induced structure formation is a common binding mechanism in aptamer-based biosensors.
- The precise mechanism of ligand-induced structural changes in aptamers remains poorly understood.
Purpose of the Study:
- To investigate the binding mechanism and ligand-induced structural changes of a dopamine-binding DNA aptamer.
- To analyze how modifications to the aptamer's terminal stem affect dopamine binding affinity and structure.
- To correlate aptamer structural dynamics with the performance of electrochemical aptamer-based biosensors.
Main Methods:
- Isothermal titration calorimetry (ITC) to quantify binding thermodynamics.
- Circular dichroism (CD) spectroscopy to assess structural changes.
- Nuclear magnetic resonance (NMR) spectroscopy (¹H NMR) to probe structural dynamics and identify ligand-induced alterations.
- Systematic modification of the aptamer's terminal stem length.
Main Results:
- All studied aptamers bind dopamine through an enthalpically driven process with unfavorable entropy.
- A decrease in binding affinity was observed as the terminal stem length of the aptamer was shortened.
- Ligand binding induced the formation of new structures in the aptamer, evidenced by ¹H NMR signals.
- Functional electrochemical aptamer-based biosensors were achieved only when the structure-forming region was proximal to the sensor surface.
Conclusions:
- The terminal stem length significantly influences the binding affinity of dopamine DNA aptamers.
- Ligand binding induces specific structural rearrangements in DNA aptamers.
- Proximity of aptamer structure-forming regions to the sensor surface is critical for developing functional electrochemical aptamer-based biosensors.
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