Photochemical and Logic-Based Regulation over the Cellular Microenvironment

Thesis (Ph.D.)--University of Washington, 2020The biological microenvironment is a complex, constantly changing space featuring varying amounts of many cell-secreted signaling molecules that serve as the communicatory elements of biology. By better understanding how well-defined combinations of individual biochemical signals including proteins presented in this space operate in (a)synchrony to direct cellular and integrated tissue function, we can begin to unravel irregularities within diseased systems and utilize this information to engineer therapies that promote healthy recovery. As photochemical reactions can be uniquely modulated in time and space, this dissertation develops and subsequently exploits novel light-based strategies to spatiotemporally control biochemical microenvironments and cellular signaling. First, we establish the cytocompatibility of near-ultraviolet light treatments common to photochemical manipulation through mammalian cell survival assays and global proteomic analyses. Expanding on existing concepts of photoresponsive drug delivery, we then introduce a generalizable strategy to govern biochemical signal presentation within biomaterials in response to precise combinations of environmental factors following user-programmable Boolean logic. Finally, we introduce the first genetically encoded protein-protein photoligation chemistry, and demonstrate its utility in irreversibly directing protein binding, function, and interactions both intra- and extracellularly. Employing this versatile photoreaction, we demonstrate 3D patterned immobilization of full-length proteins within biomaterials and user-guided intracellular protein activity. Such newly afforded 4D control over biological systems is expected to further basic biological understanding and advance medicine through enhanced tissue engineering and therapeutic delivery approaches