Churcher Zachary R, Neves Miguel A D, Hunter Howard N, Johnson Philip E
Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, ON, M3J 1P3, Canada.
Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada.
J Biomol NMR. 2017 May;68(1):33-39. doi: 10.1007/s10858-017-0112-y. Epub 2017 May 5.
Using NMR magnetization transfer experiments, the hydrogen exchange rate constants (k ) 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 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 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 values of nucleotides located away from the binding site are only minimally affected by ligand binding.
利用核磁共振磁化转移实验，已测定了可卡因结合适体中DNA亚氨基质子在游离态、可卡因结合态和奎宁结合态下的氢交换速率常数（k）。可卡因结合适体的二级结构由围绕一个三叉接头构建的三个茎组成。在游离适体中，交换最慢的亚氨基质子位于茎的中部。在茎3的GAA环中的一个核苷酸以及形成三叉接头结构的茎末端和串联GA错配中的核苷酸发现了最高的k值。配体结合后，配体结合位点处核苷酸的k值降低，表明这些碱基对在结合态下变得更稳定或溶剂可及性更低。远离结合位点的核苷酸的亚氨基质子k值仅受到配体结合的最小影响。
