UCLA

Biological imaging has transformed our understanding of life at the molecular and cellular levels. By enabling real-time visualization of dynamic processes, it has driven major breakthroughs in both fundamental research and clinical practice. Among the available imaging modalities, fluorescence imaging stands at the forefront for its exceptional sensitivity in living systems. These advantages are amplified in the near-infrared (NIR, 700–1000 nm) and shortwave infrared (SWIR, 1000–2000 nm) regions of the electromagnetic spectrum, where reduced autofluorescence and minimal light scattering enable deeper, clearer imaging. Polymethine dyes have emerged as the leading fluorophore scaffold for NIR imaging due to their high brightness, low toxicity, and tunable optical properties. Many derivatives have advanced into applications involving environmental sensing and triggered payload release. However, translating these strengths into the SWIR region presents the significant challenge of increasing absorption wavelengths while preserving brightness. This dissertation focuses on the development of new polymethine scaffolds for enhanced SWIR imaging, while also advancing the design of responsive NIR fluorophores for real-time detection in biological systems.Chapter One is a perspective that outlines key strategies for advancing SWIR polymethine dye design, including chain extension, heterocycle modification and water solubility, and frames the central challenges and opportunities that motivate the work presented in subsequent chapters. Chapter Two builds directly on these design principles through the development of a new class of silicon-containing flavylium (SiliFlav) polymethine dyes. Incorporation of a silicon heteroatom into the flavylium scaffold yields bathochromic shifts of up to 200 nm while preserving respectable fluorescence quantum yields. A modular synthetic approach allows for fine-tuning of photophysical properties through functionalization at key positions on the heterocycle. The lead compound, SiliFlav5, formulated into oil-based nanoemulsions, demonstrates strong chemical stability, low cytotoxicity, and bright SWIR emission above 1300 nm. In vivo imaging in mice reveals high-resolution visualization of vasculature and spleen, establishing SiliFlav dyes as a robust new platform for deep-tissue SWIR imaging. Chapter Three is a perspective that explores the transformation of polymethine dyes from traditional NIR fluorophores into dynamic, responsive tools for biological imaging and intervention. This includes the development of fluorogenic probes activated by specific cellular conditions and photocages capable of controlled release of bioactive molecules. These advances highlight the shift toward chemically responsive dye platforms for real-time sensing and targeted therapeutic applications. Building on this theme of responsive NIR fluorophores, Chapter Four introduces a new class of far-red to NIR flavylium merocyanine dyes that favor the fluorescent cyanine state under biologically relevant conditions. Unlike traditional scaffolds, these dyes are responsive to solvent viscosity and hydrogen bonding rather than polarity. Their unique photophysical properties enable intrinsic labeling of the endoplasmic reticulum and lipid droplets in live cells with minimal spectral crosstalk, offering a red-shifted, structurally simple alternative to conventional ER stains. Chapter Five focuses on small molecule photocages for light-triggered drug release in photoactivated chemotherapy (PACT). To meet the demands of clinical translation, this work targets photocages that are aqueous-soluble, biologically stable, oxygen-independent, and NIRactivated. A 𝜋𝜋-extended silicon coumarin scaffold incorporating a flavylium donor is proposed to overcome the limited tissue penetration of traditional coumarin systems. Synthetic efforts toward this platform reveal key structure–reactivity relationships, including the role of a 7-dimethylamino substituent in promoting non-canonical oxidation pathways. These insights inform the future design of clinically viable photocages for targeted therapeutic applications.