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Title: Self-assembled DNA cages
Author: Erben, Christoph Michael
ISNI:       0000 0001 3448 6182
Awarding Body: University of Oxford
Current Institution: University of Oxford
Date of Award: 2007
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We have investigated the construction of molecular cages from DNA. Polyhedral, nanometre-sized cages can be formed by self-assembly from synthetic DNA oligonucleotides (oligos). In this thesis, we demonstrate the encapsulation of a single molecule of the protein cytochrome c inside a DNA tetrahedron. Each edge of the tetrahedron is a 20 base pair (bp) DNA double helix with a length of 7 nm. The DNA tetrahedron is a rigid, hollow, three-dimensional structure; it forms in a single self-assembly step. Encapsulation is achieved by tethering the protein to a specific site on one of the constituent oligos and then letting the tetrahedron assemble around the protein. We show that the single-step assembly strategy of the DNA tetrahedron can be extended to larger, more complex polyhedra. We have formed a regular trigonal bipyramid from six synthetic DNA oligos. The identity of the bipyramid has been verified and the different patterns of catenanes that result from ligating a subset of the constituent oligos in the bipyramid have been analysed. In the regular tetrahedron and bipyramid, each 20-bp edge corresponds to two full turns of the pNA double helix. The design of polyhedra with different edge lengths leads to interesting topological problems and oligos are forced to cross each other at a vertex. We have analysed the formation of tetrahedra with different edge lengths and different topologies. We also present a new method for linking DNA to protein molecules. It is based on the interaction between a DNA oligo modified with three molecules of nitrilotriacetic acid (TrisNTA) and a protein carrying a hexa-histidine-tag ((His)6tag). The TrisNTA linker is easily synthesised, site-specific and could be applied to form a reversible bond to a large number of proteins. We demonstrate binding of His-tagged green fluorescent protein to a number of TrisNTA modified DNA motifs.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available