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

Mateusz Mieczkowski, Christian Steinmetzger, Irene Bessi, Ann-Kathrin Lenz, Alexander Schmiedel, Marco Holzapfel, Christoph Lambert (), Vladimir Pena () and Claudia Höbartner ()
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Mateusz Mieczkowski: Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie
Christian Steinmetzger: Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie
Irene Bessi: Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie
Ann-Kathrin Lenz: Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie
Alexander Schmiedel: Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie
Marco Holzapfel: Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie
Christoph Lambert: Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie
Vladimir Pena: Max Planck Institute for Biophysical Chemistry
Claudia Höbartner: Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie

Nature Communications, 2021, vol. 12, issue 1, 1-11

Abstract: Abstract 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 π-π 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 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.

Date: 2021
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DOI: 10.1038/s41467-021-23932-0

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