Synthesis and biophysical studies of nucleic acid-binding oligomers

In general, this thesis describes the design, synthesis, oligomerization and biophysical studies of novel PNA monomers. Our initial aim was to develop an efficient and inexpensive route for the synthesis of a series of novel alkyne PNA monomers bearing thymine, cytosine, adenine and guanine nucleobases suitable for Fmoc solid phase PNA synthesis strategy. These novel monomers allow functionalising the PNA sequences with alkyne functions at their Nterminus during solid phase synthesis. These novel monomers can be exploited in the click reaction applications such as a click ligation of PNA and conjugation of PNA with different substrates such as nucleic acids and proteins. As an application for ligation PNA sequences, the alkyne thymine PNA monomer was incorporated successfully into the target PNA oligomers during oligomerization. Mimicking the click (CuAAC) reaction linkers of the ligation of PNA oligomers, three novel 1,2,3-triazole functionalised building blocks were designed and prepared suitable for the Fmoc solid phase PNA synthesis strategy. Furthermore, synthesis of these building blocks specifically that is bearing thymine base represents an attempt for modification the original PNA oligomers in order to improve their drawbacks such as poor water solubility and cellular uptake or to enhance their hybridization properties. Our approach to synthesise these monomers is the Click (CuAAC) reaction which is not analogous for the routes that are used for the synthesis of the modified or unmodified PNA monomers. To investigate their effect on the biophysical properties of PNA oligomers, a single monomeric unit of these monomers was incorporated successfully into a series of mixed purine-pyrimidine 8-mer PNA sequences following the standard Fmoc-solid phase PNA synthesis conditions. In general, The Tm experiments-UV spectroscopy showed that the modified PNA oligomers containing these modified monomers still have a binding affinity with complementary sequences of DNA and RNA. The Tm values indicated that the incorporation of the 1,2,3-triazole functionalised monomers maintained or slightly reduced the thermal stability of the PNA/DNA duplexes, whereas the PNA/RNA duplexes resulted in a significantly reduced thermal stability. All of them are compared to the corresponding unmodified PNA/DNA duplexes