@article{ChoiKotthoffOlejkoetal.2018,
  author    = {Choi, Youngeun and Kotthoff, Lisa and Olejko, Lydia and Resch-Genger, Ute and Bald, Ilko},
  title     = {DNA origami-based forster resonance energy-transfer Nanoarrays and their application as ratiometric sensors},
  series = {ACS applied materials \& interfaces},
  volume    = {10},
  journal   = {ACS applied materials \& interfaces},
  number    = {27},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1944-8244},
  doi       = {10.1021/acsami.8b03585},
  pages     = {23295 -- 23302},
  year      = {2018},
  abstract  = {DNA origami nanostructures provide a platform where dye molecules can be arranged with nanoscale accuracy allowing to assemble multiple fluorophores without dye-dye aggregation. Aiming to develop a bright and sensitive ratiometric sensor system, we systematically studied the optical properties of nanoarrays of dyes built on DNA origami platforms using a DNA template that provides a high versatility of label choice at minimum cost. The dyes are arranged at distances, at which they efficiently interact by Forster resonance energy transfer (FRET). To optimize array brightness, the FRET efficiencies between the donor fluorescein (FAM) and the acceptor cyanine 3 were determined for different sizes of the array and for different arrangements of the dye molecules within the array. By utilizing nanoarrays providing optimum FRET efficiency and brightness, we subsequently designed a ratiometric pH nanosensor using coumarin 343 as a pH-inert FRET donor and FAM as a pH responsive acceptor. Our results indicate that the sensitivity of a ratiometric sensor can be improved simply by arranging the dyes into a well-defined array. The dyes used here can be easily replaced by other analyte-responsive dyes, demonstrating the huge potential of DNA nanotechnology for light harvesting, signal enhancement, and sensing schemes in life sciences.},
  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}
}