Quantitative Chemical Imaging in Living Systems

Our lab has generated a highly versatile functional imaging platform that utilizes DNA nanotechnology to chemically map sub-cellular structures known as organelles. We seek to answer fundamental questions such as how the chemical composition of an organelle, which has been optimized over evolutionary timescales, impacts its function at the sub-cellular level. How do these changes alter cell function, tissue function, and organism physiology? We utilize bionanotechnology to investigate these questions by exploiting our understanding of cellular machinery to develop solutions to problems in science and engineering. Our research takes advantage of nucleic acid structure and dynamics to create DNA-based nanodevices for quantitative chemical imaging of living systems.


Image: Rhod-5F, one of the fluorescent dyes we can attach to our DNA nanodevices.




Implementation of Ion Sensors in Organelles






  • Mapping pH of the Endosomal Pathway


  • The endosomal pathway contains early endosomes, late endosomes, and lysosomes. It is a highly dynamic environment used for transporting cargo into various cellular compartments. With the creation of the I-switch, our lab measured the pH of various compartments along the endosomal pathway to further understand how pH is related to the maturation of endosomes within the cell.




  • Focusing on Lysosomes and Recycling Endosomes


  • Lysosomes are a key player in the endosomal pathway and are responsible for the breakdown of biological material within cellular environments. Our work has led to the characterization of lysosomal lumenal pH and chloride, as well as reactive species such as hypochlorous acid (HOCL). Recently, we have also uncovered the sodium and calcium levels of this organelle, as well as elucidating a mechanism for calcium entry into the lysosome. In the recycling endosome, another step along the endosomal pathway, we have used our DNA nanodevices to quantify parameters such as pH, chloride, potassium, and membrane potential.




  • The Trans-Golgi Network


  • The trans-Golgi network (TGN) contributes to the sorting, modifying, and tagging of proteins from the endoplasmic reticulum and is part of the retrograde pathway. We once again deployed the I-switch to measure pH in the TGN. We have also used another nanodevice, NOckout, to measure NO levels and uncover the mechanisms of Nitric oxide synthase 3 (NOS3). Recently, with the creation of pHlicKer, we have measured potassium levels within the TGN in a pH-independent manner.
  • Yamuna Krishnan

    Email: yamuna@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.