Functional DNA nanostructures for molecular transportation and biosensing

Abstract

In this thesis, DNA nanostructures were constructed with the DNA origami method and their ability to function as stimuli-responsive nanoscale devices and molecular transport vehicles was studied. DNA origami structures can be utilized e.g. in the development of biosensing techniques and biomedical applications. For this, their functionality, suitability for the transportation and encapsulation of cargo, and structural stability in physiological conditions need to be thoroughly characterized. In the first experimental part of the work, two pH-responsive DNA origami devices were designed and their functionality was studied: DNA nanocapsules for molecular transportation and zipper-like DNA origami structures for biosensor development. Spectroscopic and electrochemical methods were applied to confirm that the conformational state of the devices could be controlled accurately and repeatedly with the solution pH by functionalizing the devices site-specifically with DNA triplexes. For studying molecular transportation, the nanocapsules were loaded with gold nanoparticles and enzymes, and an encapsulation and display of the loaded cargo could be induced by changing the solution pH. In addition, the binding of the anticancer drug doxorubicin to DNA origami structures was characterized, yielding improved understanding on how DNA origami structures can be harnessed for transportation of DNA intercalators. Finally, the structural stability of the developed DNA origami nanocarriers under destabilizing physiological factors was studied. The nanocapsule was shown to remain functional in physiologically relevant salt conditions. The nuclease digestion rates of doxorubicin-loaded DNA origami structures depended both on the DNA origami superstructure and the doxorubicin loading density, yielding doxorubicin release at customizable rates. The detailed biophysical and biochemical characterization of functional DNA origami nanostructures presented in this thesis will help building a solid ground for the development of DNA nanostructure –based applications.