Porphyrin substituted DNA: building blocks for novel nanostructures

Abstract

Porphyrin-modified DNA duplexes have been studied in detail for the last 10 years. It is well known that G-rich DNA sequences of the type (GGGX)4 can form stable intramolecular quadruplex structures containing stacks of G quartets in the presence of monovalent cations such as potassium. The synthesis of novel G-quadruplex forming DNA sequences based on the human telomeric repeat (GGGTTA)x where porphyrins are covalently attached to thymidine is presented. It is shown that the porphyrin modification offers a large degree of stabilisation to the G-quadruplex. Structural studies have revealed that the porphyrin modification does not bias the formation of a single G quadruplex. However, one exception was observed for a G quadruplex with two porphyrin modifications. Further insight into the interactions between the porphyrin and the G-quadruplex were achieved by molecular dynamic simulations. The synthesis of novel porphyrin-modified locked nucleic acids (LNA) is presented. It was hoped that the LNA modification would provide stability to the porphyrin-modified DNA duplex as porphyrin modifications have previously been found to destabilise duplex DNA. The structure and stability of the DNA was assessed in detail using circular dichroism spectroscopy. Finally, a new method of synthesising porphyrin-modified DNA using polymerases to incorporate porphyrin triphosphates into oligonucleotides is presented. The synthesis of novel porphyrin triphosphates is described. A variety of polymerases were assessed on whether they could incorporate these triphosphates into oligonucleotides. Multiple incorporations of these porphyrin-modified triphosphates showed that they were a good substrate for certain polymerases and with further development this method could be a viable route to synthesis of porphyrin-modified DNA.

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Identifiers

ORCID for Eugen Stulz: orcid.org/0000-0002-5302-2276

ORCID for Keith R. Fox: orcid.org/0000-0002-2925-7315

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