@phdthesis{Choi2018,
  author    = {Choi, Youngeun},
  title     = {DNA origami structures as versatile platforms for nanophotonics},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-421483},
  school      = {Universit{\"a}t Potsdam},
  pages     = {125},
  year      = {2018},
  abstract  = {Nanophotonics is the field of science and engineering aimed at studying the light-matter interactions on the nanoscale. One of the key aspects in studying such optics at the nanoscale is the ability to assemble the material components in a spatially controlled manner. In this work, DNA origami nanostructures were used to self-assemble dye molecules and DNA coated plasmonic nanoparticles. Optical properties of dye nanoarrays, where the dyes were arranged at distances where they can interact by F{\"o}rster resonance energy transfer (FRET), were systematically studied according to the size and arrangement of the dyes using fluorescein (FAM) as the donor and cyanine 3 (Cy 3) as the acceptor. The optimized design, based on steady-state and time-resolved fluorometry, was utilized in developing a ratiometric pH sensor with pH-inert coumarin 343 (C343) as the donor and pH-sensitive FAM as the acceptor. This design was further applied in developing a ratiometric toxin sensor, where the donor C343 is unresponsive and FAM is responsive to thioacetamide (TAA) which is a well-known hepatotoxin. The results indicate that the sensitivity of the ratiometric sensor can be improved by simply arranging the dyes into a well-defined array. The ability to assemble multiple fluorophores without dye-dye aggregation also provides a strategy to amplify the signal measured from a fluorescent reporter, and was utilized here to develop a reporter for sensing oligonucleotides. By incorporating target capturing sequences and multiple fluorophores (ATTO 647N dye molecules), a reporter for microbead-based assay for non-amplified target oligonucleotide sensing was developed. Analysis of the assay using VideoScan, a fluorescence microscope-based technology capable of conducting multiplex analysis, showed the DNA origami nanostructure based reporter to have a lower limit of detection than a single stranded DNA reporter. Lastly, plasmonic nanostructures were assembled on DNA origami nanostructures as substrates to study interesting optical behaviors of molecules in the near-field. Specifically, DNA coated gold nanoparticles, silver nanoparticles, and gold nanorods, were placed on the DNA origami nanostructure aiming to study surface-enhanced fluorescence (SEF) and surface-enhanced Raman scattering (SERS) of molecules placed in the hotspot of coupled plasmonic structures.},
  language  = {en}
}
@phdthesis{Olejko2017,
  author    = {Olejko, Lydia},
  title     = {F{\"o}rster resonance energy transfer (FRET)-based nanophotonics using DNA origami structures},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-396747},
  school      = {Universit{\"a}t Potsdam},
  year      = {2017},
  abstract  = {The field of nanophotonics focuses on the interaction between electromagnetic radiation and matter on the nanometer scale. The elements of nanoscale photonic devices can transfer excitation energy non-radiatively from an excited donor molecule to an acceptor molecule by F{\"o}rster resonance energy transfer (FRET). The efficiency of this energy transfer is highly dependent on the donor-acceptor distance. Hence, in these nanoscale photonic devices it is of high importance to have a good control over the spatial assembly of used fluorophores. Based on molecular self-assembly processes, various nanostructures can be produced. Here, DNA nanotechnology and especially the DNA origami technique are auspicious self-assembling methods. By using DNA origami nanostructures different fluorophores can be introduced with a high local control to create a variety of nanoscale photonic objects. The applications of such nanostructures range from photonic wires and logic gates for molecular computing to artificial light harvesting systems for artificial photosynthesis. In the present cumulative doctoral thesis, different FRET systems on DNA origami structures have been designed and thoroughly analyzed. Firstly, the formation of guanine (G) quadruplex structures from G rich DNA sequences has been studied based on a two-color FRET system (Fluorescein (FAM)/Cyanine3 (Cy3)). Here, the influences of different cations (Na+ and K+), of the DNA origami structure and of the DNA sequence on the G-quadruplex formation have been analyzed. In this study, an ion-selective K+ sensing scheme based on the G-quadruplex formation on DNA origami structures has been developed. Subsequently, the reversibility of the G-quadruplex formation on DNA origami structures has been evaluated. This has been done for the simple two-color FRET system which has then been advanced to a switchable photonic wire by introducing additional fluorophores (FAM/Cy3/Cyanine5 (Cy5)/IRDye®700). In the last part, the emission intensity of the acceptor molecule (Cy5) in a three-color FRET cascade has been tuned by arranging multiple donor (FAM) and transmitter (Cy3) molecules around the central acceptor molecule. In such artificial light harvesting systems, the excitation energy is absorbed by several donor and transmitter molecules followed by an energy transfer to the acceptor leading to a brighter Cy5 emission. Furthermore, the range of possible excitation wavelengths is extended by using several different fluorophores (FAM/Cy3/Cy5). In this part of the thesis, the light harvesting efficiency (antenna effect) and the FRET efficiency of different donor/transmitter/acceptor assemblies have been analyzed and the artificial light harvesting complex has been optimized in this respect.},
  language  = {en}
}