@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{RackwitzRankovićMilosavljevićetal.2017,
  author    = {Rackwitz, Jenny and Ranković, Miloš Lj. and Milosavljević, Aleksandar R. and Bald, Ilko},
  title     = {A novel setup for the determination of absolute cross sections for low-energy electron induced strand breaks in oligonucleotides},
  series = {The European physical journal : D, Atomic, molecular, optical and plasma physics},
  volume    = {71},
  journal   = {The European physical journal : D, Atomic, molecular, optical and plasma physics},
  publisher = {Springer},
  address   = {New York},
  issn      = {1434-6060},
  doi       = {10.1140/epjd/e2016-70608-4},
  pages     = {9},
  year      = {2017},
  abstract  = {Low-energy electrons (LEEs) play an important role in DNA radiation damage. Here we present a method to quantify LEE induced strand breakage in well-defined oligonucleotide single strands in terms of absolute cross sections. An LEE irradiation setup covering electron energies <500 eV is constructed and optimized to irradiate DNA origami triangles carrying well-defined oligonucleotide target strands. Measurements are presented for 10.0 and 5.5 eV for different oligonucleotide targets. The determination of absolute strand break cross sections is performed by atomic force microscopy analysis. An accurate fluence determination ensures small margins of error of the determined absolute single strand break cross sections sigma SSB. In this way, the influence of sequence modification with the radiosensitive 5-Fluorouracil (U-5F) is studied using an absolute and relative data analysis. We demonstrate an increase in the strand break yields of U-5F containing oligonucleotides by a factor of 1.5 to 1.6 compared with non-modified oligonucleotide sequences when irradiated with 10 eV electrons.},
  language  = {en}
}
@article{DoeringGrigorievTapioetal.2021,
  author    = {Doering, Ulrike and Grigoriev, Dmitry and Tapio, Kosti and Rosencrantz, Sophia and Rosencrantz, Ruben R. and Bald, Ilko and B{\"o}ker, Alexander},
  title     = {About the mechanism of ultrasonically induced protein capsule formation},
  series = {RSC Advances : an international journal to further the chemical sciences / Royal Society of Chemistry},
  volume    = {11},
  journal   = {RSC Advances : an international journal to further the chemical sciences / Royal Society of Chemistry},
  number    = {27},
  publisher = {RSC Publishing},
  address   = {London},
  issn      = {2046-2069},
  doi       = {10.1039/d0ra08100k},
  pages     = {16152 -- 16157},
  year      = {2021},
  abstract  = {In this paper, we propose a consistent mechanism of protein microcapsule formation upon ultrasound treatment. Aqueous suspensions of bovine serum albumin (BSA) microcapsules filled with toluene are prepared by use of high-intensity ultrasound following a reported method. Stabilization of the oil-in-water emulsion by the adsorption of the protein molecules at the interface of the emulsion droplets is accompanied by the creation of the cross-linked capsule shell due to formation of intermolecular disulfide bonds caused by highly reactive species like superoxide radicals generated sonochemically. The evidence for this mechanism, which until now remained elusive and was not proven properly, is presented based on experimental data from SDS-PAGE, Raman spectroscopy and dynamic light scattering.},
  language  = {en}
}
@article{HeckKanehiraKneippetal.2019,
  author    = {Heck, Christian and Kanehira, Yuya and Kneipp, Janina and Bald, Ilko},
  title     = {Amorphous Carbon Generation as a Photocatalytic Reaction on DNA-Assembled Gold and Silver Nanostructures},
  series = {Molecules},
  volume    = {24},
  journal   = {Molecules},
  number    = {12},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1420-3049},
  doi       = {10.3390/molecules24122324},
  pages     = {10},
  year      = {2019},
  abstract  = {Background signals from in situ-formed amorphous carbon, despite not being fully understood, are known to be a common issue in few-molecule surface-enhanced Raman scattering (SERS). Here, discrete gold and silver nanoparticle aggregates assembled by DNA origami were used to study the conditions for the formation of amorphous carbon during SERS measurements. Gold and silver dimers were exposed to laser light of varied power densities and wavelengths. Amorphous carbon prevalently formed on silver aggregates and at high power densities. Time-resolved measurements enabled us to follow the formation of amorphous carbon. Silver nanolenses consisting of three differently-sized silver nanoparticles were used to follow the generation of amorphous carbon at the single-nanostructure level. This allowed observation of the many sharp peaks that constitute the broad amorphous carbon signal found in ensemble measurements. In conclusion, we highlight strategies to prevent amorphous carbon formation, especially for DNA-assembled SERS substrates.},
  language  = {en}
}
@misc{HeckKanehiraKneippetal.2019,
  author    = {Heck, Christian and Kanehira, Yuya and Kneipp, Janina and Bald, Ilko},
  title     = {Amorphous Carbon Generation as a Photocatalytic Reaction on DNA-Assembled Gold and Silver Nanostructures},
  series = {Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Mathematisch-Naturwissenschaftliche Reihe},
  number    = {732},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43081},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-430812},
  pages     = {10},
  year      = {2019},
  abstract  = {Background signals from in situ-formed amorphous carbon, despite not being fully understood, are known to be a common issue in few-molecule surface-enhanced Raman scattering (SERS). Here, discrete gold and silver nanoparticle aggregates assembled by DNA origami were used to study the conditions for the formation of amorphous carbon during SERS measurements. Gold and silver dimers were exposed to laser light of varied power densities and wavelengths. Amorphous carbon prevalently formed on silver aggregates and at high power densities. Time-resolved measurements enabled us to follow the formation of amorphous carbon. Silver nanolenses consisting of three differently-sized silver nanoparticles were used to follow the generation of amorphous carbon at the single-nanostructure level. This allowed observation of the many sharp peaks that constitute the broad amorphous carbon signal found in ensemble measurements. In conclusion, we highlight strategies to prevent amorphous carbon formation, especially for DNA-assembled SERS substrates.},
  language  = {en}
}
@misc{TasiorBaldDeperasińskaetal.2015,
  author    = {Tasior, Mariusz and Bald, Ilko and Deperasińska, Irena and Cywiński, Piotr J. and Gryko, Daniel T.},
  title     = {An internal charge transfer-dependent solvent effect in V-shaped azacyanines},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-102704},
  pages     = {11714 -- 11720},
  year      = {2015},
  abstract  = {New V-shaped non-centrosymmetric dyes, possessing a strongly electron-deficient azacyanine core, have been synthesized based on a straightforward two-step approach. The key step in this synthesis involves palladium-catalysed cross-coupling of dibromo-N,N′-methylene-2,2′-azapyridinocyanines with arylacetylenes. The resulting strongly polarized π-expanded heterocycles exhibit green to orange fluorescence and they strongly respond to changes in solvent polarity. We demonstrate that differently electron-donating peripheral groups have a significant influence on the internal charge transfer, hence on the solvent effect and fluorescence quantum yield. TD-DFT calculations confirm that, in contrast to the previously studied bis(styryl)azacyanines, the proximity of S1 and T2 states calculated for compounds bearing two 4-N,N-dimethylaminophenylethynyl moieties establishes good conditions for efficient intersystem crossing and is responsible for its low fluorescence quantum yield. Non-linear properties have also been determined for new azacyanines and the results show that depending on peripheral groups, the synthesized dyes exhibit small to large two-photon absorption cross sections reaching 4000 GM.},
  language  = {en}
}
@article{TasiorBaldDeperasinskaetal.2015,
  author    = {Tasior, Mariusz and Bald, Ilko and Deperasinska, Irena and Cywinski, Piotr J. and Gryko, Daniel T.},
  title     = {An internal charge transfer-dependent solvent effect in V-shaped azacyanines},
  series = {Organic \& biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry},
  volume    = {13},
  journal   = {Organic \& biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry},
  number    = {48},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1477-0520},
  doi       = {10.1039/c5ob01633a},
  pages     = {11714 -- 11720},
  year      = {2015},
  language  = {en}
}
@misc{OlejkoCywińskiBald2016,
  author    = {Olejko, Lydia and Cywiński, P. J. and Bald, Ilko},
  title     = {An ion-controlled four-color fluorescent telomeric switch on DNA origami structures},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-95831},
  pages     = {10339 -- 10347},
  year      = {2016},
  abstract  = {The folding of single-stranded telomeric DNA into guanine (G) quadruplexes is a conformational change that plays a major role in sensing and drug targeting. The telomeric DNA can be placed on DNA origami nanostructures to make the folding process extremely selective for K+ ions even in the presence of high Na+ concentrations. Here, we demonstrate that the K+-selective G-quadruplex formation is reversible when using a cryptand to remove K+ from the G-quadruplex. We present a full characterization of the reversible switching between single-stranded telomeric DNA and G-quadruplex structures using F{\"o}rster resonance energy transfer (FRET) between the dyes fluorescein (FAM) and cyanine3 (Cy3). When attached to the DNA origami platform, the G-quadruplex switch can be incorporated into more complex photonic networks, which is demonstrated for a three-color and a four-color FRET cascade from FAM over Cy3 and Cy5 to IRDye700 with G-quadruplex-Cy3 acting as a switchable transmitter.},
  language  = {en}
}
@article{OlejkoCywinskiBald2016,
  author    = {Olejko, Lydia and Cywinski, P. J. and Bald, Ilko},
  title     = {An ion-controlled four-color fluorescent telomeric switch on DNA origami structures},
  series = {Nanoscale},
  volume    = {8},
  journal   = {Nanoscale},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {2040-3364},
  doi       = {10.1039/c6nr00119j},
  pages     = {10339 -- 10347},
  year      = {2016},
  abstract  = {The folding of single-stranded telomeric DNA into guanine (G) quadruplexes is a conformational change that plays a major role in sensing and drug targeting. The telomeric DNA can be placed on DNA origami nanostructures to make the folding process extremely selective for K+ ions even in the presence of high Na+ concentrations. Here, we demonstrate that the K+-selective G-quadruplex formation is reversible when using a cryptand to remove K+ from the G-quadruplex. We present a full characterization of the reversible switching between single-stranded telomeric DNA and G-quadruplex structures using Forster resonance energy transfer (FRET) between the dyes fluorescein (FAM) and cyanine3 (Cy3). When attached to the DNA origami platform, the G-quadruplex switch can be incorporated into more complex photonic networks, which is demonstrated for a three-color and a four-color FRET cascade from FAM over Cy3 and Cy5 to IRDye700 with G-quadruplex-Cy3 acting as a switchable transmitter.},
  language  = {en}
}