Reduction in Dynamics of Base pair Opening upon Ligand Binding by the Cocaine-Binding Aptamer.

ABSTRACT: 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°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 imin

SUBMITTER: Churcher ZR 

PROVIDER: S-EPMC7499103 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature