@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}
}
@article{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 = {Scientific Reports},
  journal   = {Scientific Reports},
  number    = {9},
  publisher = {Macmillan Publishers Limited},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-019-41136-x},
  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}
}
@article{SchmidtSchierackGerberetal.2020,
  author    = {Schmidt, Carsten and Schierack, Peter and Gerber, Ulrike and Schroeder, Christian and Choi, Youngeun and Bald, Ilko and Lehmann, Werner and R{\"o}diger, Stefan},
  title     = {Streptavidin homologues for applications on solid surfaces at high temperatures},
  series = {Langmuir},
  volume    = {36},
  journal   = {Langmuir},
  number    = {2},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {0743-7463},
  doi       = {10.1021/acs.langmuir.9b02339},
  pages     = {628 -- 636},
  year      = {2020},
  abstract  = {One of the most commonly used bonds between two biomolecules is the bond between biotin and streptavidin (SA) or streptavidin homologues (SAHs). A high dissociation constant and the consequent high-temperature stability even allows for its use in nucleic acid detection under polymerase chain reaction (PCR) conditions. There are a number of SAHs available, and for assay design, it is of great interest to determine as to which SAH will perform the best under assay conditions. Although there are numerous single studies on the characterization of SAHs in solution or selected solid phases, there is no systematic study comparing different SAHs for biomolecule-binding, hybridization, and PCR assays on solid phases. We compared streptavidin, core streptavidin, traptavidin, core traptavidin, neutravidin, and monomeric streptavidin on the surface of microbeads (10-15 mu m in diameter) and designed multiplex microbead-based experiments and analyzed simultaneously the binding of biotinylated oligonucleotides and the hybridization of oligonucleotides to complementary capture probes. We also bound comparably large DNA origamis to capture probes on the microbead surface. We used a real-time fluorescence microscopy imaging platform, with which it is possible to subject samples to a programmable time and temperature profile and to record binding processes on the microbead surface depending on the time and temperature. With the exception of core traptavidin and monomeric streptavidin, all other SA/SAHs were suitable for our investigations. We found hybridization efficiencies close to 100\% for streptavidin, core streptavidin, traptavidin, and neutravidin. These could all be considered equally suitable for hybridization, PCR applications, and melting point analysis. The SA/SAH-biotin bond was temperature sensitive when the oligonucleotide was mono-biotinylated, with traptavidin being the most stable followed by streptavidin and neutravidin. Mono-biotinylated oligonucleotides can be used in experiments with temperatures up to 70 degrees C. When oligonucleotides were bis-biotinylated, all SA/SAH-biotin bonds had similar temperature stability under PCR conditions, even if they comprised a streptavidin variant with slower biotin dissociation and increased mechanostability.},
  language  = {en}
}