To quantify analytes in subcellular organelles, we encode the device with targeting information that can localize the nucleic acid device to a specific subcellular organelle. Diverse pathogenic cargo or molecular cargo that the cell needs for its survival, enter the cell via specific endocytic pathways. Each pathway can be accessed by encoding the molecular programs required to engage a specific receptor or trafficking pathway. Thus, the targeting module of this class of nucleic acid nanodevices can incorporate these specific molecular signals for targeting to intracellular locations of choice.

The molecular programs for targeting are as follow:

Endocytic ligand and cognate receptor
Endocytic ligands, such as proteins like epidermal growth factor (EGF) or small molecules like folic acid, bind to their cognate receptors. In other words, the EGF receptor or the folate receptor resident at the plasma membrane is subsequently trafficked inside the cell to specific endocytic organelles

Anionic ligand-binding receptor and the negatively charged DNA backbone
DNA’s phos- phate backbone makes it polyanionic. This inherent negative charge has been exploited to target DNA devices to cells that express the anion ligand-binding receptors (ALBRs) or scavenger receptors in macrophages

Aptamers against cell surface proteins
By integrating an aptamer to the extracellular domain of a trafficking protein onto a nanodevice, one can traffic a DNA nanodevice from the extracellular milieu to a subcellular compartment

Chimera of synthetic DNA receptor
A generalizable synthetic, molecular programming strategy was outlined by us. The advantages of this strategy are that it circumvents both the need for an aptamer to a cell-surface protein as well as the need to chemically conjugate endocytic ligands to DNA nanodevices.

1. Thekkan, S., Jani, M. S., Cui, C., Zhou, G., Becker, L.*, Krishnan, Y.* "A DNA-based fluorescent reporter maps HOCl production in the maturing phagosome." Nature Chemical Biology, 2018, Doi: 10.1038/s41589-018-0176-3. PMID: 30531966.

2. Bhatia, D., Arumugam, S., Nasilowski, M., Joshi, H., Wunder, C., Chambon, V., Prakash, V., Grazon, C., Nadal, B., Maiti, P.K., Johannes, L.*, Dubertret, B.*, Krishnan, Y.* "Quantum dot-loaded monofunctionalized DNA Icosahedra for single particle tracking of endocytic pathways." Nature Nanotechnology, 2016, 11, 1112-1119. PMID: 27548358.

3. Modi, S.; Nizak, C.; Surana, S.; Halder, S.; Krishnan, Y.* “Two DNA nanomachines map pH of intersecting endocytic pathways.” Nature Nanotechnology, 2013, 8, 459. PMID: 23708428

4. Surana, S., Bhat, J.M., Koushika, S.P. and Krishnan, Y.* “An autonomous DNA nanomachine maps spatiotemporal pH changes in a multicellular living organism” Nature Communications, 2011, 2, 340. PMID: 21654640.