Nucleic acid nano-devices in live imaging

The first demonstration of a DNA nanomachine functioning inside living systems came from our group. We showed that using I-switch, one could effectively map spatiotemporal pH changes associated with endosomal maturation both in living cells as well as within cells present in a living organism. We are making quantitative reporters of second messenger concentrations within living systems that will eventually position DNA nanodevices as exciting and powerful tools for intracellular traffic.

Krishnan, Y., Bathe, M. Designer Nucleic Acids to probe and program the Cell. Trends in Cell Biol. 2012, 22, 624-633
Surana, S., Bhatt, J. M., Koushika, S.P.*, Krishnan, Y.* A DNA nanomachine maps spatial and temporal pH changes in a multicellular living organism. Nature Communications, 2011, 2, 33

Multiplexing DNA nanodevices

Eukaryotic cell function is tuned by an orchestrated network of compartments involved in uptake and secretion of various macromolecules. These compartments are functionally connected to each other via a series of controlled fusion and fission events between their membranes. One of the crucial determinants of this functional networking is the lumenal acidity of these compartments which is maintained by proton concentration, concentrations of different counter ions, membrane ion permeabilities and various ATP-dependent proton pumps. Maintenance of intraorganellar pH homeostasis is essential for protein glycosylation, protein sorting, biogenesis of secretory granules and transport along both secretory and endocytic pathways. Lack of probes reporting multiple pathways simultaneously has impeded understanding of intersection between the endocytic pathways. Therefore we have created a palette of DNA-based pH sensors compatible to various sub-cellular organelles such as the trans Golgi network (TGN), cis Golgi (CG) and endoplasmic reticulum (ER) of living cells as, each organelle has a different lumenal pH e.g., pHER is 7.2, pHCG is 6.6, while pHTGN is 6.3. We have engineered the I-switch to tune its pH responsive regime and now have I-switches specific for the ER, the Golgi and the late endosome and have successfully deployed two pH sensitive DNA nanodevices in the same live cell to measure pH in two different organelles simultaneously.

Modi, S., Nizak, C., Surana, S., Halder, S., Krishnan, Y.* Two DNA nanomachines map pH of intersecting endocytic pathways. Nature Nanotechnology, 2013, 8, 459-467

DNA Icosahedra for functional bioimaging

DNA can be used to make complex polyhedra such as an icosahedron, using a novel, modular assembly based approach. The power of this approach is that it allows the efficient encapsulation of other nanoscale entities in high yields. Many peptide based drugs cannot be delivered efficiently to their target due to degradation. Thus encapsulating them in non-leaky, programmable capsules such as DNA polyhedra might solve this problem. We have shown that this certainly works for bio-imaging agents, where FITC-dextran, a known pH-imaging agent could be encapsulated inside DNA Icosahedra and delivered effectively in a targeted manner in-vivo. We showed that post-encapsulation and post-delivery, cargo functionality was unaffected.

Bhatia, D., Surana, S., Chakraborty, S., Koushika, S. P., Krishnan, Y.* A synthetic icosahedral DNA-based host-cargo complex for functional in vivo imaging. Nature Communications, 2011, 2, 340


Nucleic acid based molecular devices Naturally occurring nucleic acid devices