A DNA nanomachine that maps spatial and temporal pH changes inside living cells


DNA nanomachines are synthetic assemblies that switch between defined molecular conformations upon stimulation by external triggers. Previously, the performance of DNA devices has been limited to in vitro applications. Here we report the construction of a DNA nanomachine called the I-switch, which is triggered by protons and functions as a pH sensor based on fluorescence resonance energy transfer (FRET) inside living cells. It is an efficient reporter of pH from pH 5.5 to 6.8, with a high dynamic range between pH 5.8 and 7. To demonstrate its ability to function inside living cells we use the I-switch to map spatial and temporal pH changes associated with endosome maturation. The performance of our DNA nanodevices inside living systems illustrates the potential of DNA scaffolds responsive to more complex triggers in sensing, diagnostics and targeted therapies in living systems.

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Figure 1: In vitro characterization of the I-switch.
Figure 2: I-switch internalization and function within endosomes of Drosophila haemocytes.
Figure 3: Spatial and temporal mapping of pH changes during endocytosis using the I-switch in living cells.
Figure 4: Protein tagging and pH mapping using the I-switch.


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The author would like to thank E. Westhof, V. Malhotra, V. Rodrigues, G.V. Shivashankar and A. Sarin for critical input, M. Gonzalez-Gaitan for the Rab-5–GFP flies, V. Rangaraju for technical assistance and the CIFF facility at NCBS. S.M. and S.M.G. thank the CSIR for Fellowships. This work was funded by the Nano Science and Technology Initiative, DST, Government of India, and the Innovative Young Biotechnologist Award, DBT (Government of India) to Y.K.

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S.M., S.M. and Y.K. conceived, designed and analysed the experiments. S.M. and S.M.G. performed the experiments. S.M. and Y.K. wrote the paper. D.G. performed time-resolved experiments. G.D.G. contributed the SR+ cell line.

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Correspondence to Yamuna Krishnan.

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Modi, S., M. G., S., Goswami, D. et al. A DNA nanomachine that maps spatial and temporal pH changes inside living cells. Nature Nanotech 4, 325–330 (2009). https://doi.org/10.1038/nnano.2009.83

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