@article{HeckPrinzDatheetal.2017,
  author    = {Heck, Christian and Prinz, Julia and Dathe, Andre and Merk, Virginia and Stranik, Ondrej and Fritzsche, Wolfgang and Kneipp, Janina and Bald, Ilko},
  title     = {Gold Nanolenses Self-Assembled by DNA Origami},
  series = {ACS Photonics},
  volume    = {4},
  journal   = {ACS Photonics},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {2330-4022},
  doi       = {10.1021/acsphotonics.6b00946},
  pages     = {1123 -- 1130},
  year      = {2017},
  abstract  = {Nanolenses are self-similar chains of metal nanoparticles, which can theoretically provide extremely high field enhancements. Yet, the complex structure renders their synthesis challenging and has hampered closer analyses so far. Here, DNA origami is used to self-assemble 10, 20, and 60 nm gold nanoparticles as plasmonic gold nanolenses (AuNLs) in solution and in billions of copies. Three different geometrical arrangements are assembled, and for each of the three designs, surface-enhanced Raman scattering (SERS) capabilities of single AuNLs are assessed. For the design which shows the best properties, SERS signals from the two different internal gaps are compared by selectively placing probe dyes. The highest Raman enhancement is found for the gap between the small and medium nanoparticle, which is indicative of a cascaded field enhancement.},
  language  = {en}
}
@article{HeckKanehiraKneippetal.2018,
  author    = {Heck, Christian and Kanehira, Yuya and Kneipp, Janina and Bald, Ilko},
  title     = {Placement of Single Proteins within the SERS Hot Spots of Self-Assembled Silver Nanolenses},
  series = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition},
  volume    = {57},
  journal   = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition},
  number    = {25},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1433-7851},
  doi       = {10.1002/anie.201801748},
  pages     = {7444 -- 7447},
  year      = {2018},
  abstract  = {This study demonstrates the bottom-up synthesis of silver nanolenses. A robust coating protocol enabled the functionalization of differently sized silver nanoparticles with DNA single strands of orthogonal sequence. Coated particles 10nm, 20nm, and 60nm in diameter were self-assembled by DNA origami scaffolds to form silver nanolenses. Single molecules of the protein streptavidin were selectively placed in the gap of highest electric field enhancement. Streptavidin labelled with alkyne groups served as model analyte in surface-enhanced Raman scattering (SERS) experiments. By correlated Raman mapping and atomic force microscopy, SERS signals of the alkyne labels of a single streptavidin molecule, from a single silver nanolens, were detected. The discrete, self-similar aggregates of solid silver nanoparticles are promising for plasmonic applications.},
  language  = {en}
}
@article{VogelEbelHecketal.2019,
  author    = {Vogel, Stefanie and Ebel, Kenny and Heck, Christian and Sch{\"u}rmann, Robin Mathis and Milosavljevic, Aleksandar R. and Giuliani, Alexandre and Bald, Ilko},
  title     = {Vacuum-UV induced DNA strand breaks},
  series = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  volume    = {21},
  journal   = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  number    = {4},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1463-9076},
  doi       = {10.1039/c8cp06813e},
  pages     = {1972 -- 1979},
  year      = {2019},
  abstract  = {Radiation therapy is a basic part of cancer treatment. To increase the DNA damage in carcinogenic cells and preserve healthy tissue at the same time, radiosensitizing molecules such as halogenated nucleobase analogs can be incorporated into the DNA during the cell reproduction cycle. In the present study 8.44 eV photon irradiation induced single strand breaks (SSB) in DNA sequences modified with the radiosensitizer 5-bromouracil (U-5Br) and 8-bromoadenine ((8Br)A) are investigated. U-5Br was incorporated in the 13mer oligonucleotide flanked by different nucleobases. It was demonstrated that the highest SSB cross sections were reached, when cytosine and thymine were adjacent to U-5Br, whereas guanine as a neighboring nucleobase decreases the activity of U-5Br indicating that competing reaction mechanisms are active. This was further investigated with respect to the distance of guanine to U-5Br separated by an increasing number of adenine nucleotides. It was observed that the SSB cross sections were decreasing with an increasing number of adenine spacers between guanine and U-5Br until the SSB cross sections almost reached the level of a non-modified DNA sequence, which demonstrates the high sequence dependence of the sensitizing effect of U-5Br. (8Br)A was incorporated in a 13mer oligonucleotide as well and the strand breaks were quantified upon 8.44 eV photon irradiation in direct comparison to a non-modified DNA sequence of the same composition. No clear enhancement of the SSB yield of the modified in comparison to the non-modified DNA sequence could be observed. Additionally, secondary electrons with a maximum energy of 3.6 eV were generated when using Si as a substrate giving rise to further DNA damage. A clear enhancement in the SSB yield can be ascertained, but to the same degree for both the non-modified DNA sequence and the DNA sequence modified with (8Br)A.},
  language  = {en}
}
@misc{HeckMichaeliBaldetal.2018,
  author    = {Heck, Christian and Michaeli, Yael and Bald, Ilko and Ebenstein, Yuval},
  title     = {Analytical epigenetics},
  series = {Current Opinion in Biotechnology},
  volume    = {55},
  journal   = {Current Opinion in Biotechnology},
  publisher = {Elsevier},
  address   = {London},
  issn      = {0958-1669},
  doi       = {10.1016/j.copbio.2018.09.006},
  pages     = {151 -- 158},
  year      = {2018},
  abstract  = {The field of epigenetics describes the relationship between genotype and phenotype, by regulating gene expression without changing the canonical base sequence of DNA. It deals with molecular genomic information that is encoded by a rich repertoire of chemical modifications and molecular interactions. This regulation involves DNA, RNA and proteins that are enzymatically tagged with small molecular groups that alter their physical and chemical properties. It is now clear that epigenetic alterations are involved in development and disease, and thus, are the focus of intensive research. The ability to record epigenetic changes and quantify them in rare medical samples is critical for next generation diagnostics. Optical detection offers the ultimate single-molecule sensitivity and the potential for spectral multiplexing. Here we review recent progress in ultrasensitive optical detection of DNA and histone modifications.},
  language  = {en}
}
@article{VogelEbelSchuermannetal.2019,
  author    = {Vogel, Stefanie and Ebel, Kenny and Sch{\"u}rmann, Robin Mathis and Heck, Christian and Meiling, Till and Milosavljevic, Aleksandar R. and Giuliani, Alexandre and Bald, Ilko},
  title     = {Vacuum-UV and Low-Energy Electron-Induced DNA Strand Breaks},
  series = {ChemPhysChem : a European journal of chemical physics and physical chemistry},
  volume    = {20},
  journal   = {ChemPhysChem : a European journal of chemical physics and physical chemistry},
  number    = {6},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1439-4235},
  doi       = {10.1002/cphc.201801152},
  pages     = {823 -- 830},
  year      = {2019},
  abstract  = {DNA is effectively damaged by radiation, which can on the one hand lead to cancer and is on the other hand directly exploited in the treatment of tumor tissue. DNA strand breaks are already induced by photons having an energy below the ionization energy of DNA. At high photon energies, most of the DNA strand breaks are induced by low-energy secondary electrons. In the present study we quantified photon and electron induced DNA strand breaks in four different 12mer oligonucleotides. They are irradiated directly with 8.44 eV vacuum ultraviolet (VUV) photons and 8.8 eV low energy electrons (LEE). By using Si instead of VUV transparent CaF2 as a substrate the VUV exposure leads to an additional release of LEEs, which have a maximum energy of 3.6 eV and can significantly enhance strand break cross sections. Atomic force microscopy is used to visualize strand breaks on DNA origami platforms and to determine absolute values for the strand break cross sections. Upon irradiation with 8.44 eV photons all the investigated sequences show very similar strand break cross sections in the range of 1.7-2.3x10(-16) cm(2). The strand break cross sections for LEE irradiation at 8.8 eV are one to two orders of magnitude larger than the ones for VUV photons, and a slight sequence dependence is observed. The sequence dependence is even more pronounced for LEEs with energies <3.6 eV. The present results help to assess DNA damage by photons and electrons close to the ionization threshold.},
  language  = {en}
}
@article{PrinzHeckElleriketal.2016,
  author    = {Prinz, Julia and Heck, Christian and Ellerik, Lisa and Merk, Virginia and Bald, Ilko},
  title     = {DNA origami based Au-Ag-core-shell nanoparticle dimers with single-molecule SERS sensitivity},
  series = {Nanoscale},
  volume    = {8},
  journal   = {Nanoscale},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {2040-3364},
  doi       = {10.1039/c5nr08674d},
  pages     = {5612 -- 5620},
  year      = {2016},
  abstract  = {DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 10(10), which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled.},
  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}
}
@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}
}
@phdthesis{Heck2017,
  author    = {Heck, Christian},
  title     = {Gold and silver nanolenses self-assembled by DNA origami},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-409002},
  school      = {Universit{\"a}t Potsdam},
  pages     = {ix, 125},
  year      = {2017},
  abstract  = {Nanolenses are linear chains of differently-sized metal nanoparticles, which can theoretically provide extremely high field enhancements. The complex structure renders their synthesis challenging and has hampered closer analyses so far. Here, the technique of DNA origami was used to self-assemble DNA-coated 10 nm, 20 nm, and 60 nm gold or silver nanoparticles into gold or silver nanolenses. Three different geometrical arrangements of gold nanolenses were assembled, and for each of the three, sets of single gold nanolenses were investigated in detail by atomic force microscopy, scanning electron microscopy, dark-field scattering and Raman spectroscopy. The surface-enhanced Raman scattering (SERS) capabilities of the single nanolenses were assessed by labelling the 10 nm gold nanoparticle selectively with dye molecules. The experimental data was complemented by finite-difference time-domain simulations. For those gold nanolenses which showed the strongest field enhancement, SERS signals from the two different internal gaps were compared by selectively placing probe dyes on the 20 nm or 60 nm gold particles. The highest enhancement was found for the gap between the 20 nm and 10 nm nanoparticle, which is indicative of a cascaded field enhancement. The protein streptavidin was labelled with alkyne groups and served as a biological model analyte, bound between the 20 nm and 10 nm particle of silver nanolenses. Thereby, a SERS signal from a single streptavidin could be detected. Background peaks observed in SERS measurements on single silver nanolenses could be attributed to amorphous carbon. It was shown that the amorphous carbon is generated in situ.},
  language  = {en}
}
@article{PrinzHeckElleriketal.2016,
  author    = {Prinz, Julia and Heck, Christian and Ellerik, Lisa and Merk, Virginia and Bald, Ilko},
  title     = {DNA origami based Au-Ag-core-shell nanoparticle dimers with single-molecule SERS sensitivity},
  series = {Nanoscale},
  journal   = {Nanoscale},
  number    = {8},
  publisher = {RSC Publishing},
  address   = {Cambridge},
  doi       = {10.1039/C5NR08674D},
  pages     = {5612 -- 5620},
  year      = {2016},
  abstract  = {DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 1010, which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled.},
  language  = {en}
}