Recognition Mechanism of Serotonin by a G-Quadruplex-Duplex Hybrid Aptamer

Serotonin is a key neurotransmitter, and aptamer-based tools using the 44-nt Apt44 have been successfully developed for its in vitro and in vivo detection. Nevertheless, the structural basis of recognition by this aptamer remains unclear. Here we report high-resolution NMR structures of Apt38, a 6-nt truncated variant in the third loop of Apt44, in free and serotonin-bound states. Both structures reveal a two-layered antiparallel chair-type G-quadruplex core with three edgewise loops and a terminal duplex, forming a G-quadruplex–duplex hybrid structure. Serotonin binds at the G-quadruplex–duplex junction, stabilized by stacking, electrostatic attraction, hydrogen bonding, and hydrophobic contacts. Apt38 is preorganized for binding, whereas the longer third loop of Apt44 introduces conformational dynamics into the G-quadruplex scaffold, which enables a pronounced binding-triggered conformational switch in PBS buffer, explaining its sensing mechanism. Our work reveals the recognition and sensing mechanism of the serotonin aptamer and provides a framework for aptamer design in serotonin biosensing.