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Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell


DNA is a versatile scaffold for molecular sensing in living cells, and various cellular applications of DNA nanodevices have been demonstrated. However, the simultaneous use of different DNA nanodevices within the same living cell remains a challenge. Here, we show that two distinct DNA nanomachines can be used simultaneously to map pH gradients along two different but intersecting cellular entry pathways. The two nanomachines, which are molecularly programmed to enter cells via different pathways, can map pH changes within well-defined subcellular environments along both pathways inside the same cell. We applied these nanomachines to probe the pH of early endosomes and the trans-Golgi network, in real time. When delivered either sequentially or simultaneously, both nanomachines localized into and independently captured the pH of the organelles for which they were designed. The successful functioning of DNA nanodevices within living systems has important implications for sensing and therapies in a diverse range of contexts.

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Figure 1: Programming of DNA nanodevices.
Figure 2: Programmed trafficking of DNA nanomachines along two distinct endocytic pathways.
Figure 3: In cellulo performance of DNA nanomachines.
Figure 4: SimpHony of transferrin receptor and furin endocytic pathways.
Figure 5: SimpHony of organelles with altered morphology.


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The authors thank S. Mayor, D. Lilley, A. Sarin, G.V. Shivashankar and W. Shih for critical input, and the Central Imaging and Flow Facility at NCBS for imaging. The authors also thank S. Mayor for scFv libraries and the IA2.2 cell line, and J. Bonifacino and M. Marks for the Tac-furin chimera plasmids. S.M., S.S. and S.H. thank the CSIR for research fellowships. C.N. thanks NCBS for generous support of this collaboration. Y.K. thanks the Wellcome Trust–DBT India Alliance and the Innovative Young Biotechnologist Award for funding.

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Authors and Affiliations



S.M. and Y.K. conceived and designed the experiments. C.N. contributed phage display expertise. S.M. performed the in vitro and in cellulo experiments. S.S. optimized the IFu used herein, and S.H. addressed scFv–furin stability. S.M. and Y.K. analysed the data. S.M., S.S. and Y.K. co-wrote the paper and all authors commented on the manuscript.

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Correspondence to Yamuna Krishnan.

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The authors declare no competing financial interests.

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Modi, S., Nizak, C., Surana, S. et al. Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell. Nature Nanotech 8, 459–467 (2013).

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