A nanotechnology approach to DNA analysis

Abstract

This thesis describes the investigation of quantum dots and nano-structured metallic films for use in single genomic DNA analysis. The fluorescence of continuously illuminated core/shell CdSe/ZnS quantum dots (QDs) under various atmospheric conditions is investigated experimentally. Initial enhancement in fluorescence intensity is observed followed by degradation; both are highly dependent on the atmospheric conditions. Following a series of studies theories are put forward to explain these observations.

Solution mixtures of DNA strands and QDs are imaged with Atomic Force Microscopy and Fluorescence Microscopy to investigate the binding properties of DNA strands with QDs.

Gold nanovoids are fabricated for use as a substrate to provide localised enhanced fluorescence intensity of fluorescently labelled regions of DNA strands stretched and located over nanovoids as a result of resonant coupling with localised surface plasmon polariton modes. The energy and electric field distribution of localised surface plasmon polaritons is considered for various void geometries for use with fluorescently labelled DNA. The experimental fluorescence intensity profile along fluorescently labelled DNA strands stretched over glass, electrochemically grown gold and gold nanovoid substrates is compared and the fluorescence lifetime is measured. Short fluorescence lifetimes and increased intensities over gold nanovoids and a constant lifetime over glass are observed.

The results of these biophysical studies are discussed with a view for application as methods for distinguishing different DNA sequences on the nanoscale.

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