@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{SchuermannVogelEbeletal.2018,
  author    = {Sch{\"u}rmann, Robin Mathis and Vogel, Stefanie and Ebel, Kenny and Bald, Ilko},
  title     = {The physico-chemical basis of DNA radiosensitization},
  series = {Chemistry - a European journal},
  volume    = {24},
  journal   = {Chemistry - a European journal},
  number    = {41},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {0947-6539},
  doi       = {10.1002/chem.201800804},
  pages     = {10271 -- 10279},
  year      = {2018},
  abstract  = {High-energy radiation is used in combination with radiosensitizing therapeutics to treat cancer. The most common radiosensitizers are halogenated nucleosides and cisplatin derivatives, and recently also metal nanoparticles have been suggested as potential radiosensitizing agents. The radiosensitizing action of these compounds can at least partly be ascribed to an enhanced reactivity towards secondary low-energy electrons generated along the radiation track of the high-energy primary radiation, or to an additional emission of secondary reactive electrons close to the tumor tissue. This is referred to as physico-chemical radiosensitization. In this Concept article we present current experimental methods used to study fundamental processes of physico-chemical radiosensitization and discuss the most relevant classes of radiosensitizers. Open questions in the current discussions are identified and future directions outlined, which can lead to optimized treatment protocols or even novel therapeutic concepts.},
  language  = {en}
}
@phdthesis{Ebel2021,
  author    = {Ebel, Kenny},
  title     = {Quantification of low-energy electron induced single and double strand breaks in well-defined DNA sequences using DNA origami nanostructures},
  doi       = {10.25932/publishup-50449},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-504499},
  school      = {Universit{\"a}t Potsdam},
  pages     = {111},
  year      = {2021},
  abstract  = {Ionizing radiation is used in cancer radiation therapy to effectively damage the DNA of tumors leading to cell death and reduction of the tumor tissue. The main damage is due to generation of highly reactive secondary species such as low-energy electrons (LEE) with the most probable energy around 10 eV through ionization of water molecules in the cells. A simulation of the dose distribution in the patient is required to optimize the irradiation modality in cancer radiation therapy, which must be based on the fundamental physical processes of high-energy radiation with the tissue. In the present work the accurate quantification of DNA radiation damage in the form of absolute cross sections for LEE-induced DNA strand breaks (SBs) between 5 and 20 eV is done by using the DNA origami technique. This method is based on the analysis of well-defined DNA target sequences attached to DNA origami triangles with atomic force microscopy (AFM) on the single molecule level. The present work focuses on poly-adenine sequences (5'-d(A4), 5'-d(A8), 5'-d(A12), 5'-d(A16), and 5'- d(A20)) irradiated with 5.0, 7.0, 8.4, and 10 eV electrons. Independent of the DNA length, the strand break cross section shows a maximum around 7.0 eV electron energy for all investigated oligonucleotides confirming that strand breakage occurs through the initial formation of negative ion resonances. Additionally, DNA double strand breaks from a DNA hairpin 5'-d(CAC)4T(Bt-dT)T2(GTG)4 are examined for the first time and are compared with those of DNA single strands 5'-d(CAC)4 and 5'- d(GTG)4. The irradiation is made in the most likely energy range of 5 to 20 eV with an anionic resonance maximum around 10 eV independently of the DNA sequence. There is a clear difference between σSSB and σDSB of DNA single and double strands, where the strand break for ssDNA are always higher in all electron energies compared to dsDNA by the factor 3. A further part of this work deals with the characterization and analysis of new types of radiosensitizers used in chemoradiotherapy, which selectively increases the DNA damage upon radiation. Fluorinated DNA sequences with 2'-fluoro-2'-deoxycytidine (dFC) show an increased sensitivity at 7 and 10 eV compared to the unmodified DNA sequences by an enhancement factor between 2.1 and 2.5. In addition, light-induced oxidative damage of 5'-d(GTG)4 and 5'-d((CAC)4T(Bt-dT)T2(GTG)4) modified DNA origami triangles by singlet oxygen 1O2 generated from three photoexcited DNA groove binders [ANT994], [ANT1083] and [Cr(ddpd)2][BF4]3 illuminated in different experiments with UV-Vis light at 430, 435 and 530 nm wavelength is demonstrated. The singlet oxygen induced generation of DNA damage could be detected in both aqueous and dry environments for [ANT1083] and [Cr(ddpd)2][BF4]3.},
  language  = {en}
}
@misc{BaldKopyraKeller2014,
  author    = {Bald, Ilko and Kopyra, Janina and Keller, Adrian},
  title     = {On the role of fluoro-substituted nucleosides in DNA radiosensitization for tumor radiation therapy},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-73412},
  pages     = {6825 -- 6829},
  year      = {2014},
  abstract  = {Gemcitabine (2′,2′-difluorocytidine) is a well-known radiosensitizer routinely applied in concomitant chemoradiotherapy. During irradiation of biological media with high-energy radiation secondary low-energy (<10 eV) electrons are produced that can directly induce chemical bond breakage in DNA by dissociative electron attachment (DEA). Here, we investigate and compare DEA to the three molecules 2′-deoxycytidine, 2′-deoxy-5-fluorocytidine, and gemcitabine. Fluorination at specific molecular sites, i.e., nucleobase or sugar moiety, is found to control electron attachment and subsequent dissociation pathways. The presence of two fluorine atoms at the sugar ring results in more efficient electron attachment to the sugar moiety and subsequent bond cleavage. For the formation of the dehydrogenated nucleobase anion, we obtain an enhancement factor of 2.8 upon fluorination of the sugar, whereas the enhancement factor is 5.5 when the nucleobase is fluorinated. The observed fragmentation reactions suggest enhanced DNA strand breakage induced by secondary electrons when gemcitabine is incorporated into DNA.},
  language  = {en}
}
@article{BaldKellerKopyra2014,
  author    = {Bald, Ilko and Keller, Adrian and Kopyra, Janina},
  title     = {On the role of fluoro-substituted nucleosides in DNA radiosensitization for tumor radiation therapy},
  series = {RSC Advances : an international journal to further the chemical sciences},
  volume    = {4},
  journal   = {RSC Advances : an international journal to further the chemical sciences},
  number    = {13},
  publisher = {Royal Society of Chemistry},
  issn      = {2046-2069},
  doi       = {10.1039/C3RA46735J},
  pages     = {6825 -- 6829},
  year      = {2014},
  abstract  = {Gemcitabine (2′,2′-difluorocytidine) is a well-known radiosensitizer routinely applied in concomitant chemoradiotherapy. During irradiation of biological media with high-energy radiation secondary low-energy (<10 eV) electrons are produced that can directly induce chemical bond breakage in DNA by dissociative electron attachment (DEA). Here, we investigate and compare DEA to the three molecules 2′-deoxycytidine, 2′-deoxy-5-fluorocytidine, and gemcitabine. Fluorination at specific molecular sites, i.e., nucleobase or sugar moiety, is found to control electron attachment and subsequent dissociation pathways. The presence of two fluorine atoms at the sugar ring results in more efficient electron attachment to the sugar moiety and subsequent bond cleavage. For the formation of the dehydrogenated nucleobase anion, we obtain an enhancement factor of 2.8 upon fluorination of the sugar, whereas the enhancement factor is 5.5 when the nucleobase is fluorinated. The observed fragmentation reactions suggest enhanced DNA strand breakage induced by secondary electrons when gemcitabine is incorporated into DNA.},
  language  = {en}
}
@article{EbelBald2020,
  author    = {Ebel, Kenny and Bald, Ilko},
  title     = {Length and Energy Dependence of Low-Energy Electron-Induced Strand Breaks in Poly(A) DNA},
  series = {International Journal of Molecular Sciences},
  volume    = {21},
  journal   = {International Journal of Molecular Sciences},
  number    = {1},
  publisher = {Molecular Diversity Preservation International},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms21010111},
  pages     = {11},
  year      = {2020},
  abstract  = {The DNA in living cells can be effectively damaged by high-energy radiation, which can lead to cell death. Through the ionization of water molecules, highly reactive secondary species such as low-energy electrons (LEEs) with the most probable energy around 10 eV are generated, which are able to induce DNA strand breaks via dissociative electron attachment. Absolute DNA strand break cross sections of specific DNA sequences can be efficiently determined using DNA origami nanostructures as platforms exposing the target sequences towards LEEs. In this paper, we systematically study the effect of the oligonucleotide length on the strand break cross section at various irradiation energies. The present work focuses on poly-adenine sequences (d(A₄), d(A₈), d(A₁₂), d(A₁₆), and d(A₂₀)) irradiated with 5.0, 7.0, 8.4, and 10 eV electrons. Independent of the DNA length, the strand break cross section shows a maximum around 7.0 eV electron energy for all investigated oligonucleotides confirming that strand breakage occurs through the initial formation of negative ion resonances. When going from d(A₄) to d(A₁₆), the strand break cross section increases with oligonucleotide length, but only at 7.0 and 8.4 eV, i.e., close to the maximum of the negative ion resonance, the increase in the strand break cross section with the length is similar to the increase of an estimated geometrical cross section. For d(A₂₀), a markedly lower DNA strand break cross section is observed for all electron energies, which is tentatively ascribed to a conformational change of the dA₂₀ sequence. The results indicate that, although there is a general length dependence of strand break cross sections, individual nucleotides do not contribute independently of the absolute strand break cross section of the whole DNA strand. The absolute quantification of sequence specific strand breaks will help develop a more accurate molecular level understanding of radiation induced DNA damage, which can then be used for optimized risk estimates in cancer radiation therapy.},
  language  = {en}
}
@misc{EbelBald2020,
  author    = {Ebel, Kenny and Bald, Ilko},
  title     = {Length and Energy Dependence of Low-Energy Electron-Induced Strand Breaks in Poly(A) DNA},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {814},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44412},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-444125},
  pages     = {13},
  year      = {2020},
  abstract  = {The DNA in living cells can be effectively damaged by high-energy radiation, which can lead to cell death. Through the ionization of water molecules, highly reactive secondary species such as low-energy electrons (LEEs) with the most probable energy around 10 eV are generated, which are able to induce DNA strand breaks via dissociative electron attachment. Absolute DNA strand break cross sections of specific DNA sequences can be efficiently determined using DNA origami nanostructures as platforms exposing the target sequences towards LEEs. In this paper, we systematically study the effect of the oligonucleotide length on the strand break cross section at various irradiation energies. The present work focuses on poly-adenine sequences (d(A₄), d(A₈), d(A₁₂), d(A₁₆), and d(A₂₀)) irradiated with 5.0, 7.0, 8.4, and 10 eV electrons. Independent of the DNA length, the strand break cross section shows a maximum around 7.0 eV electron energy for all investigated oligonucleotides confirming that strand breakage occurs through the initial formation of negative ion resonances. When going from d(A₄) to d(A₁₆), the strand break cross section increases with oligonucleotide length, but only at 7.0 and 8.4 eV, i.e., close to the maximum of the negative ion resonance, the increase in the strand break cross section with the length is similar to the increase of an estimated geometrical cross section. For d(A₂₀), a markedly lower DNA strand break cross section is observed for all electron energies, which is tentatively ascribed to a conformational change of the dA₂₀ sequence. The results indicate that, although there is a general length dependence of strand break cross sections, individual nucleotides do not contribute independently of the absolute strand break cross section of the whole DNA strand. The absolute quantification of sequence specific strand breaks will help develop a more accurate molecular level understanding of radiation induced DNA damage, which can then be used for optimized risk estimates in cancer radiation therapy.},
  language  = {en}
}