期刊
BIOPHYSICAL JOURNAL
卷 119, 期 6, 页码 1147-1156出版社
CELL PRESS
DOI: 10.1016/j.bpj.2020.08.012
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资金
- Natural Sciences and Engineering Research Council of Canada
We have used magnetization transfer NMR experiments to measure the exchange rate constant (k(ex)) of the imino protons in the unbound, cocaine-bound, and quinine-bound forms of the cocaine-binding DNA aptamer. Both long-stem 1 (MN4) and short-stem 1 (MN19) variants were analyzed, corresponding to structures with a prefolded secondary structure and ligand-induced-folding versions of this aptamer, respectively. The k(ex) values were measured as a function of temperature from 5 to 45 degrees C to determine the thermodynamics of the base pair opening for MN4. We find that the base pairs close to the ligand-binding site become stronger upon ligand binding, whereas those located away from the binding site do not strengthen. With the buffer conditions used in this study, we observe imino H-1 signals in MN19 not previously seen, which leads us to conclude that in the free form, both stem 2 and parts of stem 3 are formed and that the base pairs in stem 1 become structured or more rigid upon binding. This is consistent with the k(ex) values for MN19 decreasing in both stem 1 and at the ligand-binding site. Based on the temperature dependence of the k(ex) values, we find that MN19 is more dynamic than MN4 in the free and both ligand-bound forms. For MN4, ligand-binding results in the reduction of dynamics that are localized to the binding site. These results demonstrate that an aptamer in which the base pairs are preformed also experiences a reduction in dynamics with ligand binding.
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