Molecular basis of signal transduction in a cortisol-binding aptamer

Understanding the molecular recognition of small molecules such as cortisol, the primary stress-related hormone, by DNA aptamers is critical for advancing molecular biosensing. It is challenging to resolve the mechanisms of this recognition at the molecular level using experiments alone, and insights from molecular simulation can complement experimental efforts. Here, all-atom molecular dynamics simulations are used to explore the conformations of the widely used 40-mer DNA (Apt 15-1a) in solution and investigate its structural response upon cortisol recognition. This 40-mer adopted a stable hairpin structure in its free state. Upon introduction of cortisol, two main binding sites were identified: one located at the loop and the other below the stem. The simulations revealed that both single and dual site occupancies are possible; however, single-site binding at the middle region is energetically more favourable. Moreover, middle-site binding induced unique conformational rearrangements in the aptamer, leading to increased sodium ion condensation in its vicinity. These coupled conformational and electrostatic changes provide molecular-level insights into how cortisol recognition can be transduced into a measurable signal in aptamer-based sensing platforms.