Actuation of DNA cages and their potential biological applications

Thesis

DNA cages are polyhedra self-assembled from synthetic oligonucleotides in a one-pot process. The main system described in this thesis is a reconfigurable, wire-framed DNA tetrahedron in nanometre-scale. On one of its vertices this tetrahedron has an overhang that can hybridise with a specific sequence of nucleic acids and open the cage.

We describe the design of a reconfigurable cage that remained closed under physiological conditions and only opened in the presence of an appropriate signal in solution. Fluorescence techniques were employed to distinguish the open and closed states of the cage.

We used flow cytometry and confocal microscopy to successfully established the open and closed states of the cage inside live cultured mammalian cells. Further experiments revealed that the DNA cage could be opened by a separately transfected signalling strand. Hybridisation between two separately transfected systems was possible. The DNA cage was then simplified to a DNA duplex so that the intracellular interactions between the two nucleic acids systems could be studied more efficiently. Microscopy images showed that the interaction occurred in membrane-bound compartments.

We describe an investigation into the use of various cellular RNAs, including full-length mRNA and tRNA-RNA fusion, to actuate the DNA cages. Choosing an appropriate cellular opening signal remains a challenge. Analysis showed that bulky cellular RNA experienced steric hindrance with the rigid DNA cage. Finally, other potential biological applications of DNA cages, such as using DNA nanostructures as the carriers for genetic therapeutic agents, were also presented.

Authors: Entwistle, N

• Publication date: 2015
• DOI: 10.5287/ora-bxg7jndma
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: Oxford University, UK
• Language: English
• Keywords: DNA cages; DNA nanotechnology
• Subjects: Biophysics; Nanomaterials