Fluorescent probes, noble metal nanoparticles and their nanocomposites : detection of nucleic acids and other biological targets

Abstract

This thesis covers the usage of fluorescent probes, noble metal nanoparticles, and their nanocomposites for applications in biological research. The use of cyanine dyes for nucleic acid detection was focused on with presentation of synthesis, characterization of the new compounds, as well as their interactions with nucleic acids, and their applications. New cyanine dyes were synthesized to produce covalently linkable derivatives based on the chemical structure of SYBR Green II. One of the new compounds showed sensitivity to RNA above its commercial predecessor. These molecules were used to detect the viral genome of echovirus 1 using in vitro assays. Furthermore, the possibility of improving the photophysical properties of the dyes was explored by synthesizing another set of molecules. With simple changes on the dye chromophore, significant improvement in the brightness, nucleic acid binding, and photostability were achieved. Based on this series, some conclusions on the structure – activity relationship were made for these dyes. In the second part of the thesis, gold nanoclusters were studied as a potential solid support for conjugation of fluorescent probes. A synthesis for a new size of monolayer para-mercaptobenzoic acid -protected gold nanocluster was developed and characterized with PAGE and NMR spectroscopy. These clusters were then used to conjugate an azatriangelium dye to the cluster surface. The developed nanocomposite showed pH sensitivity with a fluorescence turn-on happening at a low pH. This was found to be due to the electrostatic binding and release of the dye from the quenching nanocluster proximity, due to the protonation of the ligand layer of the cluster. The literature review covers some of the advances in application of such nanocomposites employing larger, plasmonic noble metal nanoparticles. While the presented experimental work does not contain their use, they represent the logical next step for this research, due to their potential for further enhancing fluorescence detection.