DNA-based mimics of membrane proteins lipid-DNA interactions determine function

Nucleic acids, particularly DNA, are used as a nanoscale building material, due to their unique controllability via complementarity of base pairing. One of the potential applications of DNA nanotechnology is creating synthetic constructs mimicking function of membrane proteins. These natural molecular machines function embedded in the lipid bilayer. Similar membrane attachment of DNA-based structures is achieved by modifying the nucleic acid with hydrophobic anchors, most commonly cholesterol. Aiming at developing a fully functional and controllable synthetic membrane construct, the first step I undertook was to understand and utilize fundamental interactions between molecules: DNA, cholesterol and lipids. Instead of starting with a complicated DNA-based model mimicking protein architecture, here I have created a set of simple systems that allowed me to examine the major interactions between involved molecules. This work describes four aspects of the DNA-lipid systems that I have built and studied experimentally. Firstly, I have analysed the effects of membrane-spanning DNA duplex on the lipids' arrangement in the pore and presented how this arrangement can be remodelled depending on the hydrophilicity of the DNA design. Secondly, I have looked at the same system from the opposite perspective - studied and prevented the distortion of the transmembrane DNA construct induced by the surrounding lipids. Thirdly, I have evaluated the importance of ions in mediating DNA-lipid interactions, reporting analysis of two electrostatic phenomena: screening and bridging. Finally, utilizing a nanoengineered four-helix structure, I discussed surfactant's influence on DNA membrane insertion efficiency, showing that aggregation of the nanostructures is one of the major factors determining their spontaneous membrane-spanning. While the understanding of phenomena in minimalistic systems is crucial for further development of complex pore-forming constructs, here I showed that even simple DNA nanostructures, when rationally designed, can mimic functionality of natural membrane proteins.