Cortisol Recognition by a Conformationally Responsive DNA Aptamer

ABSTRACT

Cortisol‐binding DNA aptamers have emerged as promising recognition elements for non‐invasive cortisol biosensing. However, the molecular basis of cortisol recognition and signal generation remains poorly understood. Here, we investigate the structural dynamics and cortisol binding behavior of the widely used 85‐nucleotide DNA aptamer, Apt15‐1, using all‐atom molecular dynamics simulations. The free aptamer supports two distinct conformational states, an open‐like state and a compact closed‐like state, which differ mainly in their tertiary structural organization while preserving the core secondary structure. These two conformations also exhibit distinct local ionic environments, suggesting a possible connection between conformational redistribution and signal generation in a biosensing context. As a result, cortisol binding is strongly dependent on aptamer conformation, and specific binding geometries influence the transition between the two states, thereby biasing the pre‐existing conformational equilibrium. Such redistribution of the conformational ensemble offers a plausible molecular basis for signal generation by altering the local ionic environment at the sensor interface. NMR measurements support the molecular dynamics simulation predictions, indicating a stable binding interaction between cortisol and the 85mer. These findings demonstrate how the full‐length 85mer aptamer architecture couples cortisol recognition to conformational and ionic changes relevant to signal generation.