UC Berkeley

Small molecules are advantageous in cell biology research for a number of reasons—they are endlessly customizable, easy to store and produce, and minimally disruptive to the cellular environment. Compared to macromolecules like proteins and oligonucleotides, they are also easy to deliver to the cell, to target to specific subcellular components, and are compatible with diverse biological systems. For similar reasons, visible light is also a wonderful tool for studying the cell— widely available, minimally invasive, and compatible with a variety of experimental conditions. The obvious combination of photoactive small molecules and visible light-based methods has led to the development of a staggering number of tools and techniques for cell biology applications. In this dissertation, I describe my contributions towards the improvement of photoactive small molecules for visible light-based cell biology methods, and the novel applications of these molecules. In chapter one, I outline the basic photophysical properties that are crucial to understanding this work. I also discuss some small molecule structures and what makes them especially well-suited to cell applications, as well as some of the most relevant visible light-based technologies and how they are being used to elucidate biological processes. In chapter two, I describe the design of and synthetic efforts towards brighter and lower-energy silicon rhodamine structures. In chapter three, I share published worked on the design and application of HMSiR680-Me, a silicon rhodamine fluorophore that selectively targets acidic organelles and is suitable for long time-lapse, multiplexed far-red nanoscopy. And in chapter four, I summarize the development of hexyl acridine orange as a photocatalytic tool for enabling mitochondrial proteomics.