Self-assembly Strategies for Functional DNA Nanostructures

Doctoral thesis, 2009

The technological revolution of the twentieth century was famously subject to Moore’s law which related the rate of growth to the ability to scale-down the size of the components – size matters. Several decades later we are, however, approaching the limit of what is possible with silicon wafers. Moreover, the world is becoming ever-more environmentally conscious and technology is no longer merited simply by its short-term possibilities but its long-term consequences are also under scrutiny. The looming implication is that we need to change the materials on which we base our technology, and improve their efficiency. There are many options available to the researchers including carbon nanotubes, the manipulation of which is briefly touched upon here. The main focus of this thesis is, however, the bio-inspired approach – using simple assemblies of DNA fragments and lipid bilayers in water – to create miniscule structures with an inbuilt function that may one day operate as a nano-device. The fact that DNA possesses an inherent molecular recognition code makes it the ideal candidate for building information-rich structures. The studies in this thesis have concentrated on building the elements of a non-repetitive two-dimensional DNA network – forming structures that are less than 10 nm in diameter and that can be functionalised with a precision of less than 1 nm. Such a network could be used as e.g. a directed energy transfer circuit. Light, pH and temperature have been used to control the structures in a predictable manner – simple energy transfer steps across the structures have also been probed and we have established that relatively small changes in pH can be used to switch on and off communication between two points in the network. The fundamental interactions between a lipid bilayer and DNA are also considered, in order to understand how best to immobilise a DNA network on such a semi-fluidic support. One important finding is that there are both different interaction geometries and binding efficiencies for varying lengths of DNA in cationic lipid complexes, which may have serious implications not just in the field of nanotechnology but in the pursuit of such lipoplexes as vectors for antisense therapeutics. A second study shows that DNA strands can be tethered to a neutral lipid membrane using a porphyrin as a hydrophobic anchor and that energy and electron transfer processes can subsequently take place within such systems.