Supramolecular helical arrangement of porphyrins along DNA : a thesis submitted in the partial fulfilment of the requirements for the degree of Doctor of Philosophy in Chemistry, Massey University, Palmerston North, New Zealand

Abstract

Porphyrins are useful chromophores and have been used in numerous biological applications including light harvesting, oxygen transport and energy transfer. DNA is a perfect template for the controlled assembly of organic chromophores. By combining DNA and porphyrins in a controlled manner we have developed a novel range of porphyrin-DNA supramolecular constructs for future applications in nanobiotechnology. A number of β-pyrrolic functionalised porphyrin precursors were synthesised to be used as building blocks in the construction of both covalently and non-covalently modified DNAs. Using these porphyrins we have created several lipophilic porphyrin-DNA complexes through non-covalent attachment methods. Using a CuI catalysed azide alkyne cycloaddition (CuAAC) reaction of azido functionalised porphyrins we have developed a versatile approach for the covalent, site specific internal porphyrin insertion into oligonucleotides in a post-synthetic manner. We have investigated a number of duplex structures where porphyrins were located in the major or minor grooves of the duplex. Additionally, porphyrins were studied as intercalating moieties when they were inserted as a bulge in the middle of the duplexes or parallel triplexes. Additionally, when porphyrins were placed in both strands of the duplex they formed a zipper type structure in the minor groove. This resulted in a significant increase in the duplex thermal stability due to the formation of porphyrin H-aggregates. UV-Vis and CD spectroscopy as well as molecular modelling were used to help understand the interactions between porphyrins in the duplex. These findings lay the foundation for the future design of artificial DNA-chromophore supramolecular architectures and for their applications in material science and nanotechnology.