Comparison of the free and ligand-bound imino hydrogen exchange rates for the cocaine-binding aptamer

Using NMR magnetization transfer experi- ments, the hydrogen exchange rate constants (kex) of the DNA imino protons in the cocaine-binding aptamer have been determined for the free, cocaine-bound, and quinine- bound states. The secondary structure of the cocaine- binding aptamer is composed of three stems built around a three-way junction. In the free aptamer the slowest exchanging imino protons are located in the middle of the stems. The highest kex values were found for a nucleotide in the GAA loop of stem 3 and for nucleotides at the end of the stems that form the three-way junction structure and in the tandem GA mismatch. Upon ligand binding, the kex values of nucleotides at the ligand binding site are reduced, indicating that these base pairs become more stable or less solvent accessible in the bound state. The imino proton kex values of nucleotides located away from the binding site are only minimally affected by ligand binding.