• Fluorogenic RNA aptamers enable live-cell RNA imaging with high spatiotemporal resolution by significantly enhancing fluorophore fluorescence upon binding.
• Structural studies reveal that many fluorogenic RNA aptamers utilize base quadruples and base triples in their fluorophore-binding sites, which are critical for ligand recognition and fluorescence activation.
• The review highlights how tertiary structure information guides rational optimization of aptamers and fluorophores, improving photophysical properties for biosensing and bioimaging applications.
• Recent aptamers such as Pepper and Clivia offer high cellular brightness, good photostability, and multiple spectral properties, expanding the RNA imaging toolbox.