The field of DNA nanotechnology offers a wide range of design strategies with which nanometer-sized structures with a desired shape, size and aspect ratio can be built. The most established techniques in the field rely on close-packed 'solid' DNA nanostructures produced with either the DNA origami or the single-stranded tile techniques. These structures depend on high-salt buffer solutions and require more material than comparable size hollow wireframe structures.
This dissertation explores the construction of hollow wireframe DNA nanostructures composed of equilateral triangles. To achieve maximal material efficiency the design is restricted to use a single DNA double helix per triangle edge. As a proof of principle, the DNA origami technique is extended to produce a series of truss structures including the flat, tetrahedral, octahedral, or irregular dodecahedral truss designs. In contrast to close packed DNA origami designs these structures fold at low-salt buffer conditions. These structures have defined cavities that may in the future be used to precisely position functional elements such as metallic nanoparticles or enzymes. The design process of these structures is simplified by a custom design software.
Next, the triangulated construction motif is extended to the single-stranded DNA tile technique. A collection of finite structures, as well as one-dimensional crystalline assemblies is explored. The ideal assembly conditions are determined experimentally and using molecular dynamics simulations. A custom design software is presented to simplify the design and handling of these structures.
At last, the cost-effective prototyping of triangulated wireframe DNA origami structures is explored. This is achieved through the introduction of single-stranded “gap” regions along the triangle edges. These gap regions are then filled using a DNA polymerase rather than by synthetic oligonucleotides. This technique also allows the mechanical transformation of these structures, which is exemplified by the transition of a bent into a straight structure upon completion of the gap filling.:Abstract v
Publications vii
Acknowledgements ix
Contents xi
Chapter 1 A short introduction into DNA nanotechnology 1
1.1 Nanotechnology 1
1.1.1 Top down 1
1.1.2 Bottom up 3
1.2 Deoxyribonucleic acid (DNA) 4
1.3 DNA Nanotechnology 6
1.3.1 Tile based assembly 9
1.3.2 DNA origami and single-stranded tiles 10
1.3.3 Some applications of DNA nanotechnology 12
1.3.4 Wireframe structures 15
1.3.5 Computational tools and DNA nanotechnology. 17
Chapter 2 Motivation and objectives 19
Chapter 3 Design and Synthesis of Triangulated DNA Origami Trusses 20
3.1 Introduction 20
3.2 Results and Discussion 21
3.2.1 Design 21
3.2.2 Nomenclature and parameters of the tube structures 23
3.2.3 Gel electrophoreses analysis 25
3.2.4 Imaging of the purified structures 26
3.2.5 Optimizing the folding conditions 28
3.2.6 Comparison to vHelix 29
3.3 Conclusions 29
3.4 Methods 30
3.4.1 Standard DNA origami assembly reaction. 30
3.4.2 Gel purification. 30
3.4.3 AFM sample preparation. 31
3.4.4 TEM sample preparation. 31
3.4.5 Instructions for mixing the staple sets. 31
Chapter 4 Triangulated wireframe structures assembled using single-stranded DNA tiles 33
4.1 Introduction 33
4.2 Results and Discussion 35
4.2.1 Designing the structures 35
4.2.2 Synthesis of test structures 37
4.2.3 Molecular dynamics simulations of 6-arm junctions 38
4.2.4 Assembly of the finite structures 40
4.2.5 Influence of salt concentration and folding times 42
4.2.6 Molecular dynamics simulations of the rhombus structure 43
4.2.7 1D SST crystals 44
4.2.8 Controlling the crystal growth 46
4.3 Conclusions 48
4.4 Methods 49
4.4.1 SST Folding 49
4.4.2 Agarose Gel Electrophoresis 49
4.4.3 tSEM Characterization 49
4.4.4 AFM Imaging 49
4.4.5 AGE-Based Folding-Yield Estimation 49
4.4.6 Molecular Dynamics Simulations 50
Chapter 5 Structural transformation of wireframe DNA origami via DNA polymerase assisted gap-filling 52
5.1 Introduction 52
5.2 Results and Discussion 54
5.2.1 Design of the Structures 54
5.2.2 Folding of Gap-Structures 56
5.2.3 Inactivation of Polymerase. 57
5.2.4 Secondary Structures. 58
5.2.5 Folding Kinetics of Gap Origami. 60
5.3 Conclusions 61
5.4 Methods 62
5.4.1 DNA origami folding 62
5.4.2 Gap filling of the wireframe DNA origami structures 63
5.4.3 Agarose gel electrophoresis 63
5.4.4 PAGE gel analysis 63
5.4.5 tSEM characterization 64
5.4.6 AFM imaging 64
5.4.7 AGE based folding-yield estimation 64
5.4.8 Gibbs free energy simulation using mfold 65
5.4.9 List of sequence for folding the DNA origami triangulated structures 65
Chapter 6 Summary and outlook 67
Appendix 69
A.1 Additional figures from chapter 369
A.2 Additional figures from chapter 4 77
A.3 Additional figures from chapter 5 111
Bibliography 127
Erklärung 138
| Identifer | oai:union.ndltd.org:DRESDEN/oai:qucosa:de:qucosa:36172 |
| Date | 18 November 2019 |
| Creators | Matthies, Michael |
| Contributors | Schmidt, Thorsten-Lars, Dietz, Stefan, Technische Universität Dresden |
| Source Sets | Hochschulschriftenserver (HSSS) der SLUB Dresden |
| Language | English |
| Detected Language | English |
| Type | info:eu-repo/semantics/publishedVersion, doc-type:doctoralThesis, info:eu-repo/semantics/doctoralThesis, doc-type:Text |
| Rights | info:eu-repo/semantics/openAccess |
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