Abstract
Lipophilic-fluorescent dyes are used as probes to study the neural pathways that wire the brain. Since these dyes are able to define neuroanatomic connections through all stages of normal and mutant development, they are currently the most comprehensive method for neurotracing. In order to efficiently trace such circuitry, it is necessary to use a diffusion-matched set of spectrally distinct dyes. The fluorescent dye molecule is composed of a fluorescent head group and two hydrocarbon chains. This thesis addresses how the molecular structure of a lipophilic-fluorescent dye affects the diffusion rate by considering both the configuration of the fluorescent head group and the hydrocarbon chain length. Since the diffusion rate may also depend on the concentration of a dye, this parameter was investigated as well. Three hypotheses were addressed by measuring these parameter independently. Each dye was measured and compared using the Diffusion Distance vs. Incubation Period technique. FRAP was also used as anotherapproach for measuring the dyes. Hypothesis I: The structure of the fluorescent head group affects the diffusion coefficient. The investigation of this hypothesis demonstrated that the fluorescent head group can affect the diffusion rate. Hypothesis II: The diffusion parameters are dependent on the applied concentration. From this investigation, the results did not support the hypothesis. Hypothesis III: The diffusion coefficient is dependent on the lengths of the hydrocarbon chains. The results from these measurements demonstrate faster diffusion rates with increasing chain length.