A red-shifted donor-acceptor hemicyanine-based probe for mitochondrial pH in live cells

pH dynamically regulates diverse cellular functions and processes. At the Inner Mitochondrial Membrane (IMM), nanoscale pH gradients generated by the Electron Transport Chain (ETC) play a critical role in contributing to mitochondrial membrane potential that drives ATP synthesis and thermogenesis. However, tools to decouple pH gradients from the overall IMM potential in living cells are limited. This study integrates a fluorescent “benzo-indole” chromophore with a pH-sensitive “phenol” moiety into a single covalent skeleton to build a sensitive, red-shifted, cell-permeable pH probe (Mito-pH2). Mito-pH2 localizes inside mitochondria with high specificity presumably to the mitochondrial inner membrane by virtue of being an amphiphilic cation and can report dynamic changes in mitochondrial pH in living cells. Our design ensures that Mito-pH2 exhibits pH-sensitive dual-excitation and dual-emission peaks enabling ratiometric pH-sensing. Further, Mito-pH2 reports an increase in pH in the pH range of 3-9 through a striking colour change from yellow to purple making it a sensitive all-purpose colorimetric pH probe. A combination of DFT calculations and spectroscopy shed light on likely sensing mechanisms including photophysics. Quantitative live-cell fluorescence imaging reveals that Mito-pH2 can detect dynamic changes in mitochondrial pH upon extracellular pH modulation with little or no measurable cytotoxicity during live imaging. Red-emitting Mito-pH2 opens new avenues of quantitative mapping of physiological mitochondrial membrane pH and significantly enhances the repertoire of environment-sensitive and low-toxicity mitochondrial probes that link mitochondrial state and micro-environment.