Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine

Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by pi-pi stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.

Automated summary

Fluorogenic RNA aptamers are synthetic RNAs that bind and activate certain fluorophores, with the Chili RNA aptamer mimicking fluorescent proteins and demonstrating high affinity for specific derivatives. By utilizing crystallography and optical spectroscopy, the structural and mechanistic basis of fluorescence activation was elucidated, showcasing ultrafast excited state proton transfer as the key mechanism. The study revealed the specific interactions between the RNA and the fluorophore, shedding light on the mode of action of the large Stokes shift fluorogenic RNA aptamer.