The state of water molecules induces changes in the topologies and interactions of G-quadruplex DNA aptamers in hydrated ionic liquid

Abstract

Herein, the effects of the bound state of water molecules were investigated on the topologies and interactions of G-quadruplex DNA aptamers by using hydrated ionic liquids (ILs). Since intracellular water molecules are generally expected to exist in the bound state and not as free molecules that exist in the typical in vitro media, we proposed hydrated ILs as potential candidates for controlling the state of water molecules. Hydrated ILs have been reported to dissolve proteins without compromising their higher-order structures. In this study, the structures and interactions of three G-quadruplex DNA aptamers (one thrombin-binding aptamer and two vascular endothelial growth factor 165-binding aptamers), with their target molecules were analyzed with circular dichroism (CD) spectroscopy and enzyme-linked oligonucleotide assay by changing the water content of hydrated cholinium dihydrogen phosphate (Hy[ch][dhp]). Hy[ch][dhp] allowed the effective dissolution of G-quadruplex DNA aptamers while maintaining their structure and binding affinity to the target molecule. The water content of Hy[ch][dhp] induced changes in the CD spectra, suggesting changes in the topology of G-quadruplex structure. Increased structural stability and binding properties indicated molecular recognition and smooth dehydration progress in Hy[ch][dhp] via regulation of the state of water molecules.