Synthesis and properties of new fluorescent dyes and dye-labelled oligonucleotides

Abstract

Fluorescence is widely used in DNA sequencing and genetic analysis. Novel fluorescence techniques for studying nucleic acids and other biologically important molecules are constantly being developed. In order to provide efficient probes with desired fluorescent properties, new fluorophores and nucleic acids labelling chemistries are required. The synthesis of various cyanine dyes derivatives is described in this thesis. Dyes were designed for NHS-ester and click chemistry labelling of oligonucleotides. Additionally the synthesis of disperse blue quencher and a 2?-mesyl-modified thymidine monomer are also presented.

A simple and convenient method of oligonucleotide labelling was developed. This method utilises the copper-catalysed 1,3-dipolar cycloaddition reaction (known as click chemistry) between alkyne-modified cyanine dyes and azide modified oligonucleotides. The conditions of the labelling were optimised and have proved efficient for solid-phase and solution-phase labelling of oligonucleotides with alkyne-functionalised dyes.

Click labelling was applied for the preparation of a series of HyBeacon probes and their fluorescence properties were investigated. The click-labelled HyBeacons were compared with HyBeacons labelled with standard cyanine dye NHS-esters showing improvements in the properties of the probes labelled by click chemistry.

The thesis also contains a detailed discussion of the photophysical properties of free cyanine dyes in solution and while attached to oligonucleotide probes.

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