Journal
JOURNAL OF BIOMOLECULAR NMR
Volume 68, Issue 1, Pages 33-39Publisher
SPRINGER
DOI: 10.1007/s10858-017-0112-y
Keywords
Aptamer function; Hydrogen exchange rate constant; Ligand binding; DNA-small molecule interactions
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Funding
- Natural Sciences and Engineering Research Council of Canada (NSERC)
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Using NMR magnetization transfer experiments, the hydrogen exchange rate constants (k (ex) ) 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 k (ex) 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 k (ex) 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 k (ex) values of nucleotides located away from the binding site are only minimally affected by ligand binding.
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