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Optimizing Stem Length To Improve Ligand Selectivity in a Structure-Switching Cocaine-Binding Aptamer.
Miguel A D Neves1, Aron A Shoara1, Oren Reinstein1
1Department of Chemistry and Centre for Research on Biomolecular Interactions, York University , Toronto, Ontario M3J 1P3, Canada.
Aptamer stem length controls structure-switching for biosensors. Modifying stem 1 length in cocaine-binding aptamers tunes selectivity, enabling quinine binding over cocaine by altering aptamer stability.
Area of Science:
- Biochemistry
- Molecular Biology
- Biosensor Technology
Background:
- Aptamer structure-function relationships are vital for aptamer-based biosensor development.
- Cocaine-binding aptamers utilize a ligand-induced structure-switching mechanism for sensing.
Purpose of the Study:
- To investigate the role of stem 1 length in the structure-switching binding mechanism of cocaine-binding aptamers.
- To determine how stem 1 length influences aptamer folding and ligand binding.
- To engineer aptamer selectivity for specific ligands by manipulating stem stability.
Main Methods:
- Systematic variation of stem 1 length in cocaine-binding aptamers (1-7 base pairs).
- Analysis of structural transitions (unfolded to folded) in relation to stem 1 elongation.
- Assessment of aptamer binding selectivity for cocaine versus quinine using modified aptamers.
Main Results:
- Stem 1 length dictates the occurrence of the structure-switching binding mechanism.
- A structural transition occurs when stem 1 elongates from 3 to 4 base pairs.
- Aptamers with a 2-base pair stem 1 exhibited selectivity for quinine over cocaine due to differential binding affinities.
Conclusions:
- Stem 1 length is a critical determinant of aptamer conformational changes and binding.
- Reducing aptamer stability by shortening stem 1 can be a strategy to tune binding selectivity.
- This approach offers a general mechanism for enhancing aptamer specificity for high-affinity ligands.
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