A Method to Map Spatiotemporal pH Changes Inside Living Cells Using a pH-Triggered DNA Nanoswitch

Part of the Methods in Molecular Biology book series (MIMB, volume 749)


A few cellular compartments maintain acidic environments in their interiors that are crucial for their proper function. Alteration in steady state organelle pH is closely linked to several diseases. Although a few probes exist to measure pH of cell compartments, each has several associated limitations. We present a high-performance pH sensor, a DNA nanoswitch, a convenient method to map spatiotemporal pH changes in endocytic pathways. DNA has been used to make a variety of nanoswitches in vitro . However, the present DNA nanoswitch functions as a pH sensing device equally efficiently intracellularly as it does in vitro. This DNA nanoswitch functions as a FRET-based pH sensor in the pH regime of 5.5–7, with high dynamic range between pH 5.8 and 7. It is efficiently engulfed by Drosophila hemocytes through endocytosis and can be used to measure the acidity of the endocytic vesicles that it marks during their maturation till their lysosomal stage.

Key words

Nanomachine I-motif FRET pH sensor Endocytosis 



We thank S. Mayor and M.G. Swetha for inputs on endocytosis assay, and the Nanoscience and Technology Initiative of the Department of Science and Technology, Govt of India (GoI). S.M. thanks the Council of Scientific and Industrial Research, GoI, for funding. Y.K. thanks the Department of Biotechnology, GoI, for the Innovative Young Biotechnologist Award and NCBS for a start-up grant.


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Biochemistry, Biophysics and BioinformaticsNational Centre for Biological SciencesBangaloreIndia

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