Porphyrin Anchored DNA: Advances in DNA Nanotechnology

Licentiate thesis, 2012

DNA nanotechnology has focused on the creation of complex structures using DNA as building blocks. DNA is an attractive construction material at the nano scale due to the self-assembly and specific base-pairing of the DNA bases, allowing the placement of functional groups with sub-nm precision. The DNA double helix is also an extremely stiff molecule, a necessity for the construction of rigid objects. By using branched DNA, the field has now reached a point where a plethora of both two- and three- dimensional structures can be created with nm precision. However, when attached to solid surfaces for imaging purposes, these structures become immobile, and lose many of the properties which made them so attractive in the first place, specifically their reversible self-assembly properties. Therefore, the construction of surface bound DNA constructs which retain their properties is of paramount importance. Increasingly the focus is now shifting toward possible applications stemming from these structures. Our approach toward applications is the use of porphyrin-DNA molecules, where a porphyrin can be attached to any thymine in the DNA sequence, via a hydrophobic linker. The porphyrin combined with the linker can act as a lipophilic anchor to lipid membranes. This anchoring is based on hydrophobic forces, and allows the DNA construct to diffuse on the membrane, retaining its properties of self-assembly. This diffusion ability was shown both for simple linear DNA and for a hexagonal structure. The number of porphyrins attaching the hexagonal structure to the membrane was varied between 1-3 anchors, showing a decrease in diffusion rate with increasing number of anchors. All these constructs bind strongly to the membrane, and it was shown that the DNA could be melted and reannealed while the porphyrin was still attached to the membrane. Liposomes covered with the hexagonal structure varied in hydration radius depending on the number of anchors, with 1 anchor yielding the biggest liposomes and 3 anchors the smallest. Consequently, with only 1 anchor, the DNA is protruding from the surface, and 3 anchors are needed to align the DNA parallel to the liposome surface. The porphyrin is not merely an anchoring functionality, as it can also act as an excellent photoexcited electron donor. Electron transfer, as detected by fluorescence quenching, was shown from a double-porphyrin binding pocket, which can bind small bi-dentate Lewis bases. The amount of fluorescence quenching correlated with the driving force for electron transfer, which is a strong indication that electron transfer from porphyrin to ligand is the cause of the quenching. The electron donor ability of the porphyrin could one day allow an irreversible modification of a surface covered with electron acceptor molecules, with a pattern that is solely determined by the placement of porphyrin molecules along the DNA structure, thereby leading to a novel nm-resolution optical lithography.