The Faculty

Focus

Our research involves understanding the structure and dynamics of unusual forms of nucleic acids and translating this knowledge to create nucleic acid-based nanodevices for applications in biology.

Biography

Born, Chennai, India, 1974
Madras University, B. Sc., 1993
Indian Institute of Science, Bangalore, M.S., 1997
Indian Institute of Science, Bangalore, PhD, 2002
University of Cambridge, UK, Postdoctoral Fellow 2001-2005
National Centre for Biological Sciences, Bangalore Fellow 2005-14
University of Chicago, Professor 2014-

Accolades

2014 Council Member, Chemistry Biology Interface, Royal Society of Chemistry
2014 AVRA Young Scientist Award
2014 Faculty of 1000 Prime, Chemical Biology
2013 Associate Editor, Nanoscale, RSC Journals
2013 Editorial Advisory Board, Bioconjugate Chemistry, ACS
2013 Shanti Swarup Bhatnagar Award, Chemical Sciences
2012 YIM-Boston Young Scientist Award
2010 Wellcome-Trust-DBT Alliance Senior Research Award
2010 BK Bachhawat Award
2010 Editorial Advisory Board, ChemBiochem, Wiley VCH
2009 Indian National Science Academy’s Young Scientist Medal
2007 Innovative Young Biotechnologist Award
2003-5 Fellow of Wolfson College, University of Cambridge, UK
2002-4 The 1851 Research Fellowship from the Royal Commission for the Exhibition of 1851
1995-6 SK Ranganathan Scholarship

Research Interests

Nucleic acid-based Molecular Devices

Bionanotechnology aims to learn from nature - to understand the structure and function of biological devices and to utilise nature's solutions in advancing science and engineering. Evolution has produced an overwhelming number and variety of biological devices that function at the nanoscale or molecular level. My lab’s central theme is one of synthetic biology, which involves taking a biological device, component or concept out of its natural cellular context and harnessing its function in a completely new setting so as to probe or reprogram the cell. Our research involves understanding the structure and dynamics of unusual forms of nucleic acids and translating this knowledge to create nucleic acid-based nanodevices for applications in biology.

Synthetic DNA nanodevices

Structural DNA nanotechnology is an emerging field that seeks to create exquisitely defined nanoscale architectures via the self-assembly of a set of carefully chosen DNA sequences. With a diameter of 2 nm and a helical periodicity of 3.5 nm, the DNA double helix is inherently a nanoscale object. The specificity and predictable affinities of Watson-Crick base pairing affords a hierarchy of molecular glues between given rods at defined locations that makes DNA an ideal nanoscale construction material. DNA nanodevices could either be rigid scaffolds in 1D, 2D or 3D that function as molecular breadboards. They could also function as switches or transducers, undergoing controlled nanomechanical motion, by exhibiting a conformational change in response to a stimulus. We create such DNA-based nanodevices for applications as high-performance ‘custom’ biosensors that intercept biochemical signals, thereby interrogating and reporting on cellular processes.

DNA-based nanomachines

DNA nanomachines are nothing but molecular switches. These are artificially designed assemblies that switch between defined conformations in response to an external cue. One of the devices made by our lab is the I-switch, which is a DNA nanomachine that undergoes a conformational change triggered by protons. Though it has proved possible to create DNA machines and rudimentary walkers, the first demonstration that they could function inside living systems came from our group. We showed that 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.

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.

 

DNA Icosahedra for functional bioimaging

3D DNA polyhedra could have applications in drug delivery given that they have hollow internal cavities in which functional macromolecules may be housed and targeted. To this end we have shown that 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.

Naturally occuring Nucleic Acid Devices:

We are also interested in understanding naturally occuring nucleic acid based devices such as non-coding RNAs. RNA is an exciting and powerful biological medium for making genetically encoded, synthetic nucleic acid architectures that can probe and program the cell.

MicroRNA Biogenesis

Several naturally occuring nucleic acid based devices are nearly entirely composed of RNA: riboswitches, ribozymes and long non-coding RNAs to name a few. We also want to understand how some of these RNA based devices function, in the hope that we may someday be able to use the lessons learned to engineer smarter synthetic devices. MicroRNAs for example, are a class of RNAs that control gene expression by either by RNA transcript degradation or translational repression. Expressions of miRNAs are highly regulated in tissues, disruption of which leads to disease. But how this regulation is achieved and maintained is still largely unknown. MiRNAs that reside on clustered or polycistronic transcripts represent a more complex case where individual miRNAs from a cluster are processed with different efficiencies despite being co-transcribed. To shed light on the regulatory mechanisms that might be operating in these cases we considered the long polycistronic primary miRNA transcript pri-miR-17-92a that contains six miRNAs with diverse function. The six miRNA domains on this cluster are differentially processed to produce varying amounts of resultant mature miRNAs in different tissues. How this is achieved is not known. We show using various biochemical and biophysical methods coupled with mutational studies that pri-miR-17-92a adopts a specific three dimensional architecture which poses a kinetic barrier to its own processing. This tertiary structure could create suboptimal protein recognition sites on the pri-miRNA cluster due to higher order structure formation.

Selected Publications

Chakraborty, S., Mehtab, S., Krishnan, Y.* The predictive power of synthetic nucleic acid technologies in RNA biology. Accounts of Chemical Research, 2014 , 47, 1710-1719.

Banerjee, A., Bhatia, D., Saminathan, A., Chakraborty, S., Kar, S., Krishnan, Y.* Controlled release of encapsulated cargo from a DNA Icosahedron using a chemical trigger. Angew. Chem. Int. Ed. 2013, 52, 6854-6857.

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.

Krishnan, Y., Bathe, M. Designer Nucleic Acids to probe and program the Cell. Trends in Cell Biol. 2012, 22, 624-633.

Chakraborty, S., Mehtab, S., Patwardhan, A.R., Krishnan, Y.* Pri-miR-17-92a transcript folds into a tertiary structure and autoregulates its processing. RNA, 2012, 18, 1014-1028.

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, 339.

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.

Krishnan, Y., Simmel. F. C. Nucleic Acid Based Molecular Devices. Angew. Chem. Int. Ed., 2011, 50, 3124 – 3156.

Modi, S., Swetha, M. G., Goswami, D., Gupta, G. D., Mayor, S., Krishnan, Y.* A DNA nanomachine that maps spatial and temporal pH changes in living cells. Nature Nanotechnology, 2009, 4, 325-330.

Bhatia, D., Mehtab, S., Krishnan, R., Indi, S.S., Basu, A., Krishnan, Y.* Icosahedral DNA nanocapsules via modular assembly. Angew. Chem. Int. Ed., 2009, 48, 4134 - 4137.