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Part I. Photocages, which are light cleavable protecting groups, are an important class of chemical tools that allow light to unmask bioactive substrates with precise spatiotemporal resolution in biological microenvironments. Due to their effectiveness in biological systems, it has become increasingly important to find logically designed photocages that can cleave under visible light and Near IR conditions, wavelengths with minimal phototoxicity and increased tissue penetration compared to ultraviolet light. The scope of this research is to both rationally design and synthesize a new class of photocage based on the BODIPY moiety, as well as to modify these photocages to absorb in region of the biological window (600-1000 nm), where tissues have maximal transparency. In chapter 1, photocages derived from meso-substituted BODIPY dyes were synthesized that release acetic acid when irradiated with green wavelengths (>500 nm). The structures of the photocages were derived by computationally searching for carbocations with low-energy diradical states as a possible indicator of nearby productive conical intersections. These photocages were found to have superior optical properties than the popular o-nitrobenzyl systems, which make them promising alternatives. The utility of these photocages in living cells was successfully demonstrated by our collaborators (Prof. Emily Smith and Aleem Syed) in cultured S2 cells. In Chapter 2, Knoevenagel type reactions were used to extend the π electron conjugation of the aromatic rings of the BODIPY photocages. This extended conjugation of these BODIPY photocages resulted in a bathochromic shift in absorbance towards red light (>600 nm) and allows cleavage using wavelengths in the biological window.

Development of light- and chemo-sensitive probes for biochemical methods