UC Berkeley

In this dissertation, nanoplasmonic optical antennae are utilized as "nanoplasmonic gene switches" for on-demand and systematic gene regulation in living systems. The plasmon resonance of nanoplasmonic gene switches is specifically tuned to the near-infrared spectral region where cells and tissues are essentially transparent. Due to their extraordinarily large surface-to-volume ratio, nanoplasmonic gene switches are ideal carriers of interfering oligonucleotides, such as antisense DNA and short interfering RNA oligonucleotides (siRNA). Interfering oligonucleotides enable direct, sequence-specific silencing of genes, but alone, lack the temporal control necessary for precise spatiotemporal manipulation. While interfering oligonucleotides are attached to nanoplasmonic gene switches, oligonucleotide functionality is inactivated. Using light illumination as a remote trigger to release free oligonucleotides and "activate" their functionality, genes can be silenced on-demand. In addition to inhibitory effects, genes are also expressed on-demand. A transcriptional pulse of target gene expression is generated using nanoplasmonic gene switches of different aspect ratios to selectively and temporally manipulate the activities of repressors and activators upstream from the target gene. In this way, the magnitude and timing of genetic activities can be systematically varied on-demand. Equipped with new nanoplasmonic tools to directly probe the intracellular space, quantitative approaches should capture many dynamic activities within the living cell that were otherwise previously impossible to detect using conventional methods.