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Updated: Feb 2, 2026
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Determination of In Vitro and Cellular Turn-on Kinetics for Fluorogenic RNA Aptamers
Published on: August 9, 2022
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A Multicolor Large Stokes Shift Fluorogen-Activating RNA Aptamer with Cationic Chromophores
Christian Steinmetzger1, Navaneethan Palanisamy2,3, Kiran R Gore4,5
1Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
Chemistry (Weinheim an Der Bergstrasse, Germany)
|November 29, 2018
Summary
Researchers developed a new RNA aptamer, Chili, that binds to a novel molecule, DMHBO+, enabling highly red-shifted fluorescence. This system mimics large Stokes shift fluorescent proteins and has potential in Förster resonance energy transfer (FRET) applications.
Area of Science:
- Biochemistry
- Molecular Biology
- Chemical Biology
Background:
- Large Stokes shift (LSS) fluorescent proteins (FPs) utilize excited state proton transfer for fluorescence emission.
- The internal 4-hydroxybenzylidene imidazolone (HBI) chromophore is key to LSS FP function.
- Developing synthetic mimics of LSS FPs is crucial for advanced biological imaging and sensing.
Purpose of the Study:
- To create a novel RNA aptamer (Chili) that induces fluorescence in non-fluorescent HBI analogues.
- To engineer HBI analogues with enhanced RNA binding affinity and reduced magnesium dependence.
- To develop a new system for Förster resonance energy transfer (FRET) applications.
Main Methods:
- Design and synthesis of novel HBI analogues with cationic aromatic side chains.
- Oxidative functionalization at the C2 position of the imidazolone to create DMHBO+.
- Characterization of the Chili aptamer-DMHBO+ complex using binding assays and fluorescence spectroscopy.
Main Results:
- The Chili aptamer induces highly Stokes-shifted emission from new HBI analogues.
- DMHBO+ binds to the Chili aptamer with a low-nanomolar dissociation constant (KD).
- The Chili-DMHBO+ complex exhibits red-shifted fluorescence emission at 592 nm.
Conclusions:
- The Chili-DMHBO+ complex effectively mimics LSS FPs.
- This system is suitable as a fluorescence donor for FRET applications.
- Potential applications include FRET-based analytical RNA systems.
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