Design of a user-controllable system for self-assembly of multiple DNA origami platforms on a 2D surface

Abstract

DNA origami, a field within DNA nanotechnology and the method used for the work done in the scope of this thesis, is a very promising way of using DNA as a material. The goal of this work was to create rectangular scaffolded DNA origami platforms with an aspect ratio 2:1 that allow predefined positioning of interaction strands to initiate self-assembly into larger structures. After computationally designing the platform with caDNAno, and analyzing the strand incorporation efficiency using canDo, the DNA origami platforms were produced following a folding protocol. For the purpose of their characterization, different methods were uses: gel electrophoresis for size estimation, concentration measurements for determining the folding yield and atomic force microscopy for visualization of proper folding.The DNA origami platforms were anchored to a lipid bilayer via cholesterol moieties and imaged using single molecule fluorescence microscopy. Binding strands were added so that freely diffusing platforms bind to each other. Single molecule fluorescence microscopy was used to observe aggregation of DNA origami platforms to larger assemblies. Partial detachment of the aggregates from the lipid bilayer as well as formation of very large conglomerates was observed. This indicates that the choice of number of interaction sites between DNA origami platforms as well as between a DNA origami platform and the lipid bilayer is crucial for a successful experiment. Alternatives to anchoring DNA rectangles via cholesterol moieties to a lipid bilayer for oligomerization purposes should be taken under consideration.