Quantitative Chemical Imaging in living systems
Our lab has created a highly versatile functional imaging platform. This technology uses short DNA duplexes of ~20-30 KDa, to chemically map lumens of organelles of live cells in culture or in vivo in genetic model organisms.-
A. Quantitative, fluorescent chemical sensors
A. Quantitative, fluorescent chemical sensors
Why develop DNA nanodevices as fluorescent reporters when a range of fluorescent proteins exist? DNA is modular, allowing the integration of independent and interdependent functionalities onto one assembly. By leveraging the 1:1 stoichiometry in DNA duplexes we can integrate multiple modules with distinct functions in precise stoichiometries onto a single DNA nanodevice. These include (1) a module that acts as fluorescent reporter of a desired analyte (2) a normalizing module for ratiometric quantitation, and (3) a targeting module that localizes the reporter in a specific organelle. We have thus made fluorescent reporters that can quantitatively image ions, reactive species as well as enzymatic activity.
read more -
B. Cell-specific and Organelle-specific Targeting
B. Cell-specific and Organelle-specific Targeting
We are passionate about inventing "targeting modules" to target DNA nanodevices to a designated organelle within a cell, or to a specific cell-type in whole organisms. These are basically trafficking motifs integrated onto DNA nanodevices that engage a cell-surface protein to then traffic DNA reporters to the desired organelle. So far, we can target every kind of endocytic organelle, the trans Golgi network and the phagosome. Along with our chemical sensors, we can now quantitatively image chemicals with accuracies were previously unattainable, in subcellular locations that were previously inaccessible. read more -
C. Fundamental biology and biomedical applications
C. Fundamental biology and biomedical applications
Using quantitative chemical imaging, we study how the lumenal chemical mileu of organelles impacts organelle function, which in turn impacts cell function and animal behavior. Examples of our discoveries include the following: showing a new role for lumenal chloride in lysosome function, discovering the first example of a lysosomal Ca2+ importer in the animal kingdom, identifying the precise timescales of membrane-initiated steroid signaling and making the first measures of the membrane potential of several types of intracellular organelles. read more
Yamuna Krishnan
Email: yamuna[at]uchicago.edu
2014 - Professor, University of Chicago
2014: Assoc Professor, National Centre for Biological Sciences (NCBS)
2009-13: Reader, NCBS, Bangalore
2005-9: Fellow, NCBS, Bangalore
2001-05: 1851 Research Fellowship, University of Cambridge, UK
2002: Ph. D., Indian Institute of Science (IISc), Bangalore,
1997: M.S., IISc, Bangalore,
1993: B. Sc. Madras University
Our lab loves exploring the rich chemistry within the living cell’s myriad reaction vessels – its organelles. How does the lumenal chemical composition of an organelle – that has been optimized over evolutionary timescales – drive the biochemistry that occurs within to impact organelle function, thereby cell function, then tissue function and finally, organism physiology? To answer this, we build quantitative chemical maps of organelle lumens using the tools of bionanotechnology. Evolution has produced an overwhelming number and variety of biological devices that function at the nanoscale or molecular level. Bionanotechnology exploits our understanding of cellular machinery to develop solutions to problems in science and engineering. Our research exploits nucleic acid structure and dynamics to create DNA-based nanodevices for quantitative chemical imaging of living systems.