Engineering fluorescent protein chromophores with an internal reference for high-fidelity ratiometric G4 imaging in living cells

G-quadruplexes (G4s) are significant nucleic acid secondary structures formed by guanine-rich sequences. Many single-emission G4 fluorescent probes that are lit up by inhibiting intramolecular rotation have been reported. However, they are non-fluorescent unless structurally rigidified, making them sensitive to other intracellular crowding and confinement environments in the cell, like viscosity. Ratiometric measurements provide built-in self-calibration for signal correction, enabling more sensitive and reliable detection. Herein, we structurally modulate green fluorescent protein (GFP)-like chromophores by integrating the imidazolidinone scaffold of the GFP chromophore and coumarin 6H, obtaining a G4 responsive dual-emission chromophore, called NHCouI. The red emission signal of NHCouI can specifically respond to parallel G4s, while its green emission signal is inert and acts as an internal reference signal. NHCouI–G4 complexes feature high fluorescence quantum yield and excellent anti-photobleaching properties. NHCouI can self-calibrate the signal and avoid viscosity disturbances within the range of major subcellular organelles during G4 imaging in living cells. It is also applied to reflect the difference between apoptosis and ferroptosis via tracking G4s. To the best of our knowledge, NHCouI is the first small molecule G4 probe enabled by internal reference correction capability, opening up new avenues for dual-emission chromophore development and high-fidelity and reliable analysis in G4 imaging research.