First As Probe, Then As Function - Fluorescence in Bio-inspired Nanotechnology

Doctoral thesis, 2012

In this thesis, I demonstrate how fluorescence can be used in the context of bio-inspired nanotechnology, both as an indirect probe and as a function in itself. By combining principles and molecules from three different bio-molecular systems, DNA, bacterial light-harvesting complexes and cell membranes, I have constructed nano- and microscale systems for long-range excitation energy transfer, light-harvesting and reaction control. In the first part of the work, DNA is utilized as a scaffold for fluorophores, arranged in a manner that facilitates excitation energy transfer from either one end of a wire to the other, or from a single input to two separate outputs in a nanoscale DNA network. These photonic assemblies use Pacific Blue and Cy3 as input and output fluorophores, respectively. The network also comprises fluorescein as an alternative output. Both systems rely on the intercalator YO-PRO-1 to mediate energy transfer between input and output. With this design, it is possible to construct a 20-mer wire with over 90% end-to-end efficiency and a longer 50-mer wire that enables energy transfer over more than 20 nm. In the network, it is possible to regulate the flow of excitation energy between the two spatially and spectrally separate outputs. In the second part, a DNA-based light-harvesting complex is presented. By loading the DNA scaffold with intercalators it is possible to enhance the excitation of a membrane-anchored porphyrin acceptor through energy transfer from the YO-PRO-1 donors. Using a linear and a hexagonal light-harvesting complex the excitation of the acceptor porphyrin can be enhanced by a factor of 13 and 18, respectively. Finally in the third part, lipid monolayer films with incorporated DNA molecules are created on hydrophobic substrates. DNA moves inside the film and can therefore interact and form duplexes with complementary strands also incorporated in the film. This process is studied in patterned surfaces where the mixing of lipid films is restricted by the shape of the hydrophobic support. The hybridization mechanism is investigated using single molecule fluorescence spectroscopy, showing that the duplex formation rate depends on the length of the DNA strand.