Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways

Abstract

Functionalization of quantum dots (QDs) with a single biomolecular tag using traditional approaches in bulk solution has met with limited success. DNA polyhedra consist of an internal void bounded by a well-defined three-dimensional structured surface. The void can house cargo and the surface can be functionalized with stoichiometric and spatial precision. Here, we show that monofunctionalized QDs can be realized by encapsulating QDs inside DNA icosahedra and functionalizing the DNA shell with an endocytic ligand. We deployed the DNA-encapsulated QDs for real-time imaging of three different endocytic ligands—folic acid, galectin-3 (Gal3) and the Shiga toxin B-subunit (STxB). Single-particle tracking of Gal3- or STxB-functionalized QD-loaded DNA icosahedra allows us to monitor compartmental dynamics along endocytic pathways. These DNA-encapsulated QDs, which bear a unique stoichiometry of endocytic ligands, represent a new class of molecular probes for quantitative imaging of endocytic receptor dynamics.

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Figure 1: Encapsulation of QDs within DNA icosahedra.
Figure 2: Cellular validation of atomistic model of the DNA icosahedron.
Figure 3: Binding of IQDGal3 to the plasma membranes of cells.
Figure 4: TEM studies reveal that IQDGal3 is endocytosed through CLICs.
Figure 5: Single-particle tracking of IQDSTxB in live cells.

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Acknowledgements

The authors thank S. Surana and T. Pons for discussions and suggestions. The imaging facilities CIFF at NCBS and PICT-IBiSA / Nikon Imaging Centre at the Institut Curie-CNRS and the France-BioImaging infrastructure (ANR-10-INSB-04) are acknowledged. D.B. thanks CEFIPRA for the Charpak Fellowship, the Institute Curie and HFSP for postdoctoral fellowships. This work was supported by the following grants: 4803-B from CEFIPRA to B.D. and Y.K.; RGP0029/2014 from HFSP to Y.K. and L.J.; Agence Nationale pour la Recherche ANR-09-BLAN-283 from FPGG to B.D. and L.J.; ANR-11 BSV2 014 03 to L.J.; project 340485 from the European Research Council to L.J.; UL1 TR000430 from the National Center for Advancing Translational Sciences of the NIH and start-up support from the University of Chicago to Y.K. The Johannes team is members of Labex CelTisPhyBio (11-LBX-0038) and of Idex Paris Sciences et Lettres (ANR-10-IDEX-0001-02 PSL).

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D.B. and Y.K. conceived the project and designed experiments; D.B. performed all experiments, some collaboratively. C.W., M.N., S.A., C.G. and B.N. contributed reagents and tools. S.A., V.P. and V.C. performed key experiments. H.J. and P.K.M. designed and performed molecular dynamics. D.B., C.W., P.K.M., L.J., B.D. and Y.K. designed experiments and analysed data. D.B., L.J. and Y.K. co-wrote the manuscript. All of the authors discussed the results and the manuscript.

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Correspondence to Ludger Johannes or Benoit Dubertret or Yamuna Krishnan.

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Competing interests

B.D. is also associated with NexDot, a for-profit company that provided the QDs used in this collaborative study.

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Bhatia, D., Arumugam, S., Nasilowski, M. et al. Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways. Nature Nanotech 11, 1112–1119 (2016). https://doi.org/10.1038/nnano.2016.150

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