Charge-elimination strategy for constructing RNA-selective fluorescent probe undisturbed by mitochondria

Visualizing Ribonucleic acid (RNA) dynamics inside live cells is crucially important for the research of life science. However, almost all of the reported RNA probes target RNA with cationic groups, and mitochondria with high negative transmembrane potential may bring significant interferences. As a result, precise visualization of RNA in living cells is still a greatly challenging task. To overcome this problem, in this work, we proposed a novel charge-elimination strategy to construct a fluorescent probe (H-SMBT) specific for RNA undisturbed by mitochondria in live cells. Probe H-SMBT was designed to target the negative groove of RNA with a cationic group, and an additional hydroxyl group was modified to overcome the interference from mitochondria. H-SMBT will change from cationic structure to a charge-eliminated state in mitochondria with weak alkalic environment and detach from mitochondria, and therefore, it can exclusively stain RNA in live cells. Using M-SMBT with a methoxy group as a comparative molecule, we confirmed that the phenol group in H-SMBT played a decisive role to achieve the RNA specificity. Furthermore, H-SMBT can fast stain live cells in 5 min with excellent RNA selectivity. The probe can also monitor cellular damage processes, and successfully be applied to live zebrafish imaging due to the good tissue permeability. This work provides a new design strategy for constructing RNA-selective fluorescent probes avoiding the interference from mitochondria, and the designed RNA probe can be widely used for RNA-related life science research.