Quinine Binding by the Cocaine-Binding Aptamer. Thermodynamic and Hydrodynamic Analysis of High-Affinity Binding of an Off-Target Ligand
| dc.contributor.author | Reinstein, Oren | |
| dc.contributor.author | Yoo, Mina | |
| dc.contributor.author | Han, Chris | |
| dc.contributor.author | Palmo, Tsering | |
| dc.contributor.author | Beckham, Simone A | |
| dc.contributor.author | Wilce, Matthew CJ | |
| dc.contributor.author | Johnson, Philip E | |
| dc.date.accessioned | 2023-05-11T16:36:27Z | |
| dc.date.available | 2023-05-11T16:36:27Z | |
| dc.date.issued | 2013-10-31 | |
| dc.description.abstract | The cocaine-binding aptamer is unusual in that it tightly binds molecules other than the ligand it was selected for. Here, we study the interaction of the cocaine-binding aptamer with one of these off-target ligands, quinine. Isothermal titration calorimetry was used to quantify the quinine-binding affinity and thermodynamics of a set of sequence variants of the cocaine-binding aptamer. We find that the affinity of the cocaine-binding aptamer for quinine is 30−40 times stronger than it is for cocaine. Competitive binding studies demonstrate that both quinine and cocaine bind at the same site on the aptamer. The ligand-induced structural-switching binding mechanism of an aptamer variant that contains three base pairs in stem 1 is retained with quinine as a ligand. The short stem 1 aptamer is unfolded or loosely folded in the free form and becomes folded when bound to quinine. This folding is confirmed by NMR spectroscopy and by the short stem 1 construct having a more negative change in heat capacity of quinine binding than is seen when stem 1 has six base pairs. Small-angle X-ray scattering (SAXS) studies of the free aptamer and both the quinine- and the cocaine-bound forms show that, for the long stem 1 aptamers, the three forms display similar hydrodynamic properties, and the ab initio shape reconstruction structures are very similar. For the short stem 1 aptamer there is a greater variation among the SAXS-derived ab initio shape reconstruction structures, consistent with the changes expected with its structural-switching binding mechanism. | en_US |
| dc.identifier.citation | Biochemistry 52 (2013): 8652−8662 | en_US |
| dc.identifier.uri | https://doi.org/10.1021/bi4010039 | en_US |
| dc.identifier.uri | http://hdl.handle.net/10315/41141 | |
| dc.language.iso | en | en_US |
| dc.publisher | American Chemical Society | en_US |
| dc.rights | Attribution-NonCommercial-NoDerivatives 4.0 International | * |
| dc.rights.uri | http://creativecommons.org/licenses/by-nc-nd/4.0/ | * |
| dc.title | Quinine Binding by the Cocaine-Binding Aptamer. Thermodynamic and Hydrodynamic Analysis of High-Affinity Binding of an Off-Target Ligand | en_US |
| dc.type | Article | en_US |