Photophysical exploration of fluorescent nanotags

Fluorescence labeling technique has found many important applications such as medical diagnostics, immunoassays and direct visualization of biological molecules. The main focus of this thesis is to use various techniques to study a number of novel florescence labels named nanotag, with the goal of constructing a fluorescence label that is photostable on both single molecular level and the ensemble level; that is compact in size so that it will not affect the activity of the targeted molecule; and that acts as antenna with strong light-harvesting ability.;In the fluorescence spectroscopy, Förster resonance energy transfer (FRET) is a result of the dipole-dipole interaction between a donor fluorophore and an acceptor fluorophore. FRET a useful technique to shift the excitation wavelength to a longer wavelength to minimize the background. In the thesis, the efficiencies of the FRET of a variety of fluorescence labels were explored using different FRET donor-acceptor (D-A) pairs and different D-A ratios aimed to build a superior system where high brightness can be readily achieved and where FRET efficiency has less restriction on the D-A spectral overlap.;Also, we are interested in setting up several models to quantitatively simulate the FRET calculation in various designs of nanotags consisting of an array of dyes (multichromophoric array) and in evaluating the suitability of those FRET models. Additionally, this thesis quantitatively evaluates the light harvesting ability of nanotags by examining the antenna effects (AE) defined as the intensity of the nanotag acceptors excited at the donor peak divided by the intensity of the nanotag acceptors upon direct excitation at acceptor absorption peak. Furthermore, we established a model that simulates the AE efficiency in the nanotags. This AE model shows an outstanding agreement with our experimental AE results.;Particularly, Chapter 1 introduces the main theories and concepts used in the thesis and the motivations of our experiments. Chapter 2 of the thesis provides the readers with the instrumentation set up and the experimental design. Chapter 3 explores the fluorescence quenching of the DNA-bound dyes using different sized gold nanoparticles as the quencher. Chapter 4 discusses the photophysics of a novel fluorescence label non-covalently loaded with dyes. Chapter 5 discusses the photophysics of the fluorescence labels with covalently bound the dyes.