A Method to Map Spatiotemporal pH Changes in a Multicellular Living Organism Using a DNA Nanosensor

Environmental pH has a determining role in the structure of biomolecules, thus playing an important role in regulating cellular activities. Eukaryotic cells must, therefore, strive to stringently regulate pH in various intracellular organelles so as to confer normal functioning at the level of whole organism. Several pH-sensitive probes have been reported, each of which can be used to map the pH dependence of an in vivo process. However, these probes suffer from some inherent drawbacks. Here we demonstrate the utility of an externally introduced, pH-triggered DNA nanomachine inside the multicellular eukaryote Caenorhabditis elegans . The nanomachine uses FRET to effectively map spatiotemporal pH changes associated with endocytosis in coelomocytes of wild type as well as mutant worms, in a variety of genetic backgrounds. It shows highest dynamic range in the pH regime 5.3–6.6 and has a half-life of ∼8 h, thus positioning it well to interrogate a variety of pH-correlated biological phenomena in vivo.