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

• DOI: 10.1038/s41467-021-23932-0
• Publication Date: 2021-06-10T10:04:33Z
• Authors: Mateusz Mieczkowski; Christian Steinme...; Irene Bessi; Ann-Kathrin Lenz; Alexander Schmiedel; Marco Holzapfel; Christoph Lambert; Vladimir Pena; Claudia Höbartner
• Keywords: Aptamer; Stokes shift; Chromophore; G-quadruplex

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