The rational design of complementary DNA sequences can be used to create nanostructures that self-assemble with nanometer precision. DNA nanostructures have been imaged by atomic force microscopy and ...electron microscopy. Small-angle X-ray scattering (SAXS) provides complementary structural information on the ensemble-averaged state of DNA nanostructures in solution. Here we demonstrate that SAXS can distinguish between different single-layer DNA origami tiles that look identical when immobilized on a mica surface and imaged with atomic force microscopy. We use SAXS to quantify the magnitude of global twist of DNA origami tiles with different crossover periodicities: these measurements highlight the extreme structural sensitivity of single-layer origami to the location of strand crossovers. We also use SAXS to quantify the distance between pairs of gold nanoparticles tethered to specific locations on a DNA origami tile and use this method to measure the overall dimensions and geometry of the DNA nanostructure in solution. Finally, we use indirect Fourier methods, which have long been used for the interpretation of SAXS data from biomolecules, to measure the distance between DNA helix pairs in a DNA origami nanotube. Together, these results provide important methodological advances in the use of SAXS to analyze DNA nanostructures in solution and insights into the structures of single-layer DNA origami.
We report the design and assembly of chiral DNA nanotubes with well‐defined and addressable inside and outside surfaces. We demonstrate that the outside surface can be functionalised with a chiral ...arrangement of gold nanoparticles to create a plasmonic device and that the inside surface can be functionalised with a track for a molecular motor allowing transport of a cargo within the central cavity.
Inside and out: The design and assembly of chiral DNA nanotubes with well‐ defined and addressable inside and outside surfaces is reported.
This thesis sets out to further the field of functional DNA nanotechnology through the design of novel functional DNA scaffolds, and investigates their applications and efficacy. The work presented ...here comprises two parts: The design of a chiral DNA nanotube that acts as a scaffold for motor motion and for an enzyme cascade; and the design of two different tetrahedral scaffolds for selection of a combination of three ligands, which together have a greater binding effect than the sum of the individual components. It begins by proposing the design of a DNA origami nanotube which distinguishes between the inside and outside face of the tube at the design stage, which most previous designs reported do not. The previous designs in the literature result in a distribution of 50:50, of one face forming the inside surface on one tube and the same face forming the outside surface of a different tube. In the design presented in this thesis, this distinction results from making the tube chiral, which forces it to roll up in a predetermined manner. Chirality is introduced by varying the positions of staple crossovers and this process is explained. The chiral tubes may stack end-to-end to form long polymers, or exist in monomeric form with stacking suppressed, by inclusion of different sets of staples at the ends of the tubes. We confirm tube formation and right-handed chirality with AFM and CD respectively. The efficacy of the tube as a scaffold for an enzyme cascade is tested and discussed in context of the wider field. No significant enhancement is observed when enzymes are tethered to the inside of the tubes, compared to when they are tethered to the outside or are free in solution, although the same slight trend is always observed. Suggestions are made to better this experiment and further understand the underlying physics of such systems. We propose using the tube as a scaffold for a DNA track, upon which a DNA motor may walk. DNA motors are introduced and we attempt to observe micron-scale, inter-tube motion within the confines of our origami tube. Initial experiments show the motor moving and we propose methods of fluorescent labeling via PAINT to better the experimental set-up for TIRF microscopy, which currently is limited by photobleaching. The second part of this thesis proposes systems for selection of a combination of three ligands, which together have a greater binding effect than the sum of the individual components. Here we design two tetrahedral systems where either three ligands or three aptamers are brought together at a vertex of the tetrahedron to form a binding domain. The aptameric system allows for selection, amplification and reassembly of the strongest binders, because the functional and structural sequences are on one strand of DNA, following ligation. This design betters the initial tetrahedral system, where the coding/record strands for amplification are separate from the functional binding domain strands the ligands are attached to. This means it is not possible to reassemble this particular structure after amplification of the record strand.
This thesis sets out to further the field of functional DNA nanotechnology through the design of novel functional DNA scaffolds, and investigates their applications and efficacy. The work presented ...here comprises two parts: The design of a chiral DNA nanotube that acts as a scaffold for motor motion and for an enzyme cascade; and the design of two different tetrahedral scaffolds for selection of a combination of three ligands, which together have a greater binding effect than the sum of the individual components. It begins by proposing the design of a DNA origami nanotube which distinguishes between the inside and outside face of the tube at the design stage, which most previous designs reported do not. The previous designs in the literature result in a distribution of 50:50, of one face forming the inside surface on one tube and the same face forming the outside surface of a different tube. In the design presented in this thesis, this distinction results from making the tube chiral, which forces it to roll up in a predetermined manner. Chirality is introduced by varying the positions of staple crossovers and this process is explained. The chiral tubes may stack end-to-end to form long polymers, or exist in monomeric form with stacking suppressed, by inclusion of different sets of staples at the ends of the tubes. We confirm tube formation and right-handed chirality with AFM and CD respectively. The efficacy of the tube as a scaffold for an enzyme cascade is tested and discussed in context of the wider field. No significant enhancement is observed when enzymes are tethered to the inside of the tubes, compared to when they are tethered to the outside or are free in solution, although the same slight trend is always observed. Suggestions are made to better this experiment and further understand the underlying physics of such systems. We propose using the tube as a scaffold for a DNA track, upon which a DNA motor may walk. DNA motors are introduced and we attempt to observe micron-scale, inter-tube motion within the confines of our origami tube. Initial experiments show the motor moving and we propose methods of fluorescent labeling via PAINT to better the experimental set-up for TIRF microscopy, which currently is limited by photobleaching. The second part of this thesis proposes systems for selection of a combination of three ligands, which together have a greater binding effect than the sum of the individual components. Here we design two tetrahedral systems where either three ligands or three aptamers are brought together at a vertex of the tetrahedron to form a binding domain. The aptameric system allows for selection, amplification and reassembly of the strongest binders, because the functional and structural sequences are on one strand of DNA, following ligation. This design betters the initial tetrahedral system, where the coding/record strands for amplification are separate from the functional binding domain strands the ligands are attached to. This means it is not possible to reassemble this particular structure after amplification of the record strand.
Drop-casting acetone solutions of Fe(bpp) 2 BF 4 2 (bpp = 2,6-dipyrazol-1-ylpyridine) onto a HOPG surface affords unusual chain-of-beads nanostructures. The beads in each chain are similar in size, ...with diameters in the range of 2–6 nm and heights of up to 10 Å, which is consistent with them containing between 10–50 molecules of the compound. The beads can be classified into two types, which exhibit different conduction regimes by current-imaging tunnelling spectroscopy (CITS) which appear to correlate with their positions in the chains, and may correspond to molecules containing high-spin and low-spin iron centres. Similarly drop-cast films of the complex on a gold surface contain the intact Fe(bpp) 2 BF 4 2 compound by XPS. 4-Mercapto-2,6-dipyrazol-1-ylpyridine undergoes substantial decomposition when deposited on gold, forming elemental sulfur, but 4-( N -thiomorpholinyl)-2,6-dipyrazol-1-ylpyridine successfully forms SAMs on a gold surface by XPS and ellipsometry.
We report the design and assembly of chiral DNA nanotubes with well‐defined and addressable inside and outside surfaces. We demonstrate that the outside surface can be functionalised with a chiral ...arrangement of gold nanoparticles to create a plasmonic device and that the inside surface can be functionalised with a track for a molecular motor allowing transport of a cargo within the central cavity.
Innen und außen: Entwurf und Aufbau chiraler DNA‐Nanoröhren mit definierten und ansteuerbaren inneren und äußeren Oberflächen werden beschrieben.
Drop-casting acetone solutions of Fe(bpp)
2
BF
4
2
(bpp = 2,6-dipyrazol-1-ylpyridine) onto a HOPG surface affords unusual chain-of-beads nanostructures. The beads in each chain are similar in size, ...with diameters in the range of 2-6 nm and heights of up to 10 Å, which is consistent with them containing between 10-50 molecules of the compound. The beads can be classified into two types, which exhibit different conduction regimes by current-imaging tunnelling spectroscopy (CITS) which appear to correlate with their positions in the chains, and may correspond to molecules containing high-spin and low-spin iron centres. Similarly drop-cast films of the complex on a gold surface contain the intact Fe(bpp)
2
BF
4
2
compound by XPS. 4-Mercapto-2,6-dipyrazol-1-ylpyridine undergoes substantial decomposition when deposited on gold, forming elemental sulfur, but 4-(
N
-thiomorpholinyl)-2,6-dipyrazol-1-ylpyridine successfully forms SAMs on a gold surface by XPS and ellipsometry.
Drop-casting Fe(bpp)
2
BF
4
2
(bpp = 2,6-dipyrazol-1-ylpyridine) onto HOPG affords chain-of-beads nanostructures. SAMs of bpp derivatives with sulfur-containing tethers are also described.
It started with a jeep Wall, Tony; Bathgate, Benn; Kerr, Florence
Waikato times,
10 Sep 2016
Newspaper Article
Biographical material. Source: National Library of New Zealand Te Puna Matauranga o Aotearoa, licensed by the Department of Internal Affairs for re-use under the Creative Commons Attribution 3.0 New ...Zealand Licence.
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