The primary focus of the lab is to engineer small molecules and programmable molecular materials to address challenges in bioimaging and create novel approaches for diagnostic sensing and therapeutics. We are translating concepts from synthetic chemistry into biological systems to develop novel chemical tools e.g. bioorthogonal chemistries for labeling and tracking specific biomolecules and therapeutics as they functionin vivo. We are engineering small molecules and nanoparticle based systems for performing selective chemistries in living system. Applications include selective assembly of small molecular components into distinct macromolecular structure for in vivo drug synthesis and barcoding for multiplexed biomolecule detection. We are performing additional manipulation of these systems using photochemical components to achieve spatiotemporally controlled regulation of biological processes at single cell or subcellular resolution.
In the area of programmable molecular materials, we are interested in synthetic DNA nanostructures. Our idea is to utilize their prescribed 3D geometry and large number of uniquely addressable features to organize sensor arrays for creating highly sensitive diagnostic systems. The other exciting application of this system is to employ the programmable nature of DNA hybridization to generate probes for super-resolution microscopy. Once integrated with molecular targeting techniques, this imaging method will allow in situ proteomics imaging at single cell resolution in the context of the tissue microenvironment.
Performing selective chemistries in biological systems such as in cells or in living organisms is a challenging but highly functional objective. The ability to chemically conjugate functional groups such as fluorochromes and affinity tags in a site-specific manner would allow a wide variety of biomolecules to be specifically labeled and imaged in their native cellular environment, providing an alternative to genetically encoded fluorescent protein based method. Although tagging method involving genetically encoded fluorescent proteins (e.g. GFP) have been widely used for monitoring biomolecules, the large size of the fluorescent proteins can introduce significant perturbation to the protein structure. Additionally there are many important biomolecules that are not within the reach of genetics, such as lipids, glycans, metabolites, myriad post-translational modifications and therapeutic drug molecules.
We are applying synthetic chemistry concepts to develop novel chemical tools for labeling and tracking specific biomolecules as they function in vivo. We are designing these strategies based on bioorthogonal reactions; broadly refer to the chemical reactions that can be performed in living systems without interference from the biological milieu. One example of such reaction is strain promoted cycloaddition reaction between trans-cyclooctene and tetrazine. Specifically, for live cell imaging applications we are investigating reactions with the following characteristics: high chemo-selectivity, rapid kinetics, high affinity for non-covalent bio-orthogonal pairs, cell permeability, low toxicity and fluorescence 'turn-on' upon conjugation for enhanced signal-to-background.
We are integrating photo responsive component with these systems for providing spatiotemporal control to the labeling process. To understand the dynamics of cells or even subcellular molecules, it is required to noninvasively label selected cell/cells or intracellular components in spatiotemporally controlled manner and image them over time. Our approach is light modulated labeling, as light irradiation can be easily controlled in a spatial and temporal fashion. The other area of application of this light based strategy is creating photochemical switch for regulation of biological processes at single cell or subcellular resolution.
Besides biomolecular imaging, we are exploring the ability to carry out in vivo selective chemical transformations in designing new therapeutic approaches and devising new methodologies for biomarkers detection. For example, we are exploring selective assembly of small molecular components into distinct macromolecular structure for in vivo drug synthesis and therapeutic activation. We are also interested in devising new barcoding strategy for multiplexed biomolecule detection based on this assembly process.
Fluorescence microscopy is a powerful tool for exploring molecules in biological system. Specifically the invention of super resolution microscopy techniques enabled visualization of molecules beyond the diffraction limit of light. Although these techniques showed remarkable success in revealing structural details of subcellular organelles and various biomolecular organizations, the multiplexing power i.e. the number of distinct molecular species that can beimaged simultaneously of these techniques is often limited by the spectral overlap between fluorophores.
To address this challenge we are currently employing the programmable nature of DNA hybridization to generate probes for super-resolution microscopy. This imaging technique, called DNA-PAINT, accomplishes the necessary fluorescence ON/OFF switching for localization-based super-resolution microscopy by using transient DNA hybridization. Besides achieving ultra-high imaging resolution (~10 nm), this imaging technique, has an intrinsically scalable multiplexing ability (>100✕). By integrating with molecularly targeted affinity ligand (e.g. antibodies), we are interested in in situ proteomics imaging from single cells in the context of the tissue microenvironment.
An important application of this technique will be in deciphering cellular signaling network. Signaling molecules and their interactions have been at the center of investigations for years for understanding basic biology as well as for developing molecularly/pathway targeted therapies. Deciphering the cell's complex signaling pathways, however, has been challenging. The major limitation has been the lack of cellular imaging techniques that can identify and differentiate large number of distinct molecular species involved in the signaling pathways. Additionally, given the fact that most protein molecules are only a few nanometers in size, a considerably higher resolution imaging is required for directly resolving molecular interactions and clustering in cells. We are interested in employing highly multiplexed DNA based super resolution imaging technology to investigate cellular signaling network.
In the area of programmable molecular materials, we are interested in synthetic DNA nanostructures. With nucleic acid as a building block, the benefit is that molecular interactions can be precisely programmed for self-assembly purpose. This property can be harnessed to make DNA-based materials with specific 2D/3D geometry and topology, mechanical properties and uniquely addressable functionality. We are interested in exploiting the prescribed 2D/3D geometry and extraordinarily feature of large number of uniquely addressable features to organize sensor arrays for creating highly sensitive diagnostic systems.
Analyzing protein signature from single cell is gaining increasing importance in basic biological research as well as in clinical diagnostics. Single-cell measurement of proteins provides valuable insight into cellular heterogeneity, which plays an important role in disease development and progression, stem cell differentiation, and cellular response to therapeutic agents. In clinics, better understanding of tumor heterogeneity can have important implications in devising better therapeutic approaches. In diagnostics, accurate proteomic analysis of rare cells (e.g. circulating tumor cells, CTCs) holds considerable promise for early disease detection as well as monitoring treatment response.
Two important challenges in this field are 1) isolating CTCs and other rare cells from biological fluids and 2) quantitative and multiplexed protein analysis at single cell resolution. To address these challenges, we are employing a synergistic approach combining synthetic and supramolecular chemistry, programmable DNA materials and DNA molecular devices to built effective strategy for on-chip capture and analysis of single cells. We are developing technologies to efficiently capture cells on functionalized surfaces as well as release them for further analysis. Simultaneously, we are interested in developing technologies for protein detection focusing on single cell sensitivity and multiplexing capability.