@misc{ChoiSchmidtTinnefeldetal.2019,
  author    = {Choi, Youngeun and Schmidt, Carsten and Tinnefeld, Philip and Bald, Ilko and R{\"o}diger, Stefan},
  title     = {A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-naturwissenschaftliche Reihe},
  number    = {705},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42827},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-428271},
  pages     = {8},
  year      = {2019},
  abstract  = {The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to increase the binding strength of the target oligonucleotide to these nanostructures. Here we present a proof-of-concept study to quantify short oligonucleotides by developing a novel DNA origami based reporter system, combined with planar microbead assays. Analysis of the assays using the VideoScan digital imaging platform showed DNA origami to be a more suitable reporter candidate for quantification of the target oligonucleotides at lower concentrations than a conventional reporter that consists of one dye molecule attached to a single stranded DNA. Efforts have been made to conduct multiplexed analysis of different targets as well as to enhance fluorescence signals obtained from the reporters. We therefore believe that the quantification of short oligonucleotides that exist in low copy numbers is achieved in a better way with the DNA origami nanostructures as reporters.},
  language  = {en}
}
@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}
}