@phdthesis{Vogel2018,
  author    = {Vogel, Stefanie},
  title     = {Sequence dependency of photon and electron induced DNA strand breaks},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-419669},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xii, 117},
  year      = {2018},
  abstract  = {Deoxyribonucleic acid (DNA) is the carrier of human genetic information and is exposed to environmental influences such as the ultraviolet (UV) fraction of sunlight every day. The photostability of the DNA against UV light is astonishing. Even if the DNA bases have a strong absorption maximum at around 260 nm/4.77 eV, their quantum yield of photoproducts remains very low 1. If the photon energies exceed the ionization energy (IE) of the nucleobases ( ̴ 8-9 eV) 2, the DNA can be severely damaged. Photoexcitation and -ionization reactions occur, which can induce strand breaks in the DNA. The efficiency of the excitation and ionization induced strand breaks in the target DNA sequences are represented by cross sections. If Si as a substrate material is used in the VUV irradiation experiments, secondary electrons with an energy below 3.6 eV are generated from the substrate. This low energy electrons (LEE) are known to induce dissociative electron attachment (DEA) in DNA and with it DNA strand breakage very efficiently. LEEs play an important role in cancer radiation therapy, since they are generated secondarily along the radiation track of ionizing radiation. In the framework of this thesis, different single stranded DNA sequences were irradiated with 8.44 eV vacuum UV (VUV) light and cross sections for single strand breaks (SSB) were determined. Several sequences were also exposed to secondary LEEs, which additionally contributed to the SSBs. First, the cross sections for SSBs depending on the type of nucleobases were determined. Both types of DNA sequences, mono-nucleobase and mixed sequences showed very similar results upon VUV radiation. The additional influence of secondarily generated LEEs resulted in contrast in a clear trend for the SSB cross sections. In this, the polythymine sequence had the highest cross section for SSBs, which can be explained by strong anionic resonances in this energy range. Furthermore, SSB cross sections were determined as a function of sequence length. This resulted in an increase in the strand breaks to the same extent as the increase in the geometrical cross section. The longest DNA sequence (20 nucleotides) investigated in this series, however, showed smaller cross section values for SSBs, which can be explained by conformational changes in the DNA. Moreover, several DNA sequences that included the radiosensitizers 5-Bromouracil (5BrU) and 8-Bromoadenine (8BrA) were investigated and the corresponding SSB cross sections were determined. It was shown that 5BrU reacts very strongly to VUV radiation leading to high strand break yields, which showed in turn a strong sequence-dependency. 8BrA, on the other hand, showed no sensitization to the applied VUV radiation, since almost no increase in strand breakage yield was observed in comparison to non-modified DNA sequences. In order to be able to identify the mechanisms of radiation damage by photons, the IEs of certain DNA sequences were further explored using photoionization tandem mass spectrometry. By varying the DNA sequence, both the IEs depending on the type of nucleobase as well as on the DNA strand length could be identified and correlated to the SSB cross sections. The influence of the IE on the photoinduced reaction in the brominated DNA sequences could be excluded.},
  language  = {en}
}
@phdthesis{Moeser2021,
  author    = {M{\"o}ser, Christin},
  title     = {Modular DNA constructs for oligovalent bio-enhancement and functional screening},
  doi       = {10.25932/publishup-50728},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-507289},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XIV, 148},
  year      = {2021},
  abstract  = {Deoxyribonucleic acid (DNA) nanostructures enable the attachment of functional molecules to nearly any unique location on their underlying structure. Due to their single-base-pair structural resolution, several ligands can be spatially arranged and closely controlled according to the geometry of their desired target, resulting in optimized binding and/or signaling interactions. This dissertation covers three main projects. All of them use variations of functionalized DNA nanostructures that act as platform for oligovalent presentation of ligands. The purpose of this work was to evaluate the ability of DNA nanostructures to precisely display different types of functional molecules and to consequently enhance their efficacy according to the concept of multivalency. Moreover, functionalized DNA structures were examined for their suitability in functional screening assays. The developed DNA-based compound ligands were used to target structures in different biological systems. One part of this dissertation attempted to bind pathogens with small modified DNA nanostructures. Pathogens like viruses and bacteria are known for their multivalent attachment to host cells membranes. By blocking their receptors for recognition and/or fusion with their targeted host in an oligovalent manner, the objective was to impede their ability to adhere to and invade cells. For influenza A, only enhanced binding of oligovalent peptide-DNA constructs compared to the monovalent peptide could be observed, whereas in the case of respiratory syncytial virus (RSV), binding as well as blocking of the target receptors led to an increased inhibition of infection in vitro. In the final part, the ability of chimeric DNA-peptide constructs to bind to and activate signaling receptors on the surface of cells was investigated. Specific binding of DNA trimers, conjugated with up to three peptides, to EphA2 receptor expressing cells was evaluated in flow cytometry experiments. Subsequently, their ability to activate these receptors via phosphorylation was assessed. EphA2 phosphorylation was significantly increased by DNA trimers carrying three peptides compared to monovalent peptide. As a result of activation, cells underwent characteristic morphological changes, where they "round up" and retract their periphery. The results obtained in this work comprehensively prove the capability of DNA nanostructures to serve as stable, biocompatible, controllable platforms for the oligovalent presentation of functional ligands. Functionalized DNA nanostructures were used to enhance biological effects and as tool for functional screening of bio-activity. This work demonstrates that modified DNA structures have the potential to improve drug development and to unravel the activation of signaling pathways.},
  language  = {en}
}
@phdthesis{Kirste2020,
  author    = {Kirste, Matthias},
  title     = {Ruthenium(II)- und Rhenium(I)-Komplexe des 1,6,7,12-Tetraazaperylens und seiner Dimethyl- und Tetramethylderivate},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XII, 137},
  year      = {2020},
  abstract  = {Die vorliegende Dissertationsschrift mit dem Titel: „Ruthenium(II)- und Rhenium(I)-Komplexe des 1,6,7,12-Tetraazaperylens und seiner Dimethyl- und Tetramethylderivate" von Matthias Kirste wurde unter der Leitung des Herrn Prof. Dr. Hans-J{\"u}rgen Holdt am Institut f{\"u}r Chemie der Universit{\"a}t Potsdam angefertigt. Die Arbeit besch{\"a}ftigt sich mit Ruthenium(II)- und Rhenium(I)-Komplexen des großfl{\"a}chigen Liganden 1,6,7,12-Tetraazaperylen (tape) und seiner 2,11-Dimethyl-(dmtape)- und 2,5,8,11-Tetramethyl-(tmtape)-derivate. Es wurden die bekannten Herstellungen des tape- sowie des dmtape-Liganden verbessert und die Synthese des tmtape-Liganden neu entwickelt. Zudem gelang mit einer neu entwickelten chemischen Reaktion die Synthese des dianionischen 3,10-Disulfonato-1,6,7,12-tetraazaperylens. Mit dmtape und tmtape wurde jeweils ein neuer Ruthenium(II)-Komplex hergestellt. Die Komplexe wurden photophysikalisch und elektrochemisch charakterisiert. KT-DNS-Interkalationen wurden von einkernigen Ruthenium(II)-Komplexen mit jeweils tape-, dmtape- und tmtape als interkalative Einheit vermessen. Es zeigte sich, dass diese Komplexe mit einer hohen Bindungsaffinit{\"a}t in die doppelstr{\"a}ngige KT-DNS interkalieren. Aus den mononuklearen Ruthenium(II)-Komplexen gelang die Herstellung von heterodinuklearen RuIIReI-Komplexen, die charakteristische Signale in ihren UV/Vis-Absorptionsspektren zeigen und sehr leicht jeweils ein- sowie zweifach im Bereich von 70 mV bis -80 mV und -440 mV bis -600 mV vs. GKE reduzierbar sind. Diese dmtape- sowie tmtape-verbr{\"u}ckten heterodinuklearen RuIIReI-Komplexe erm{\"o}glichen eine Feinjustierung ihrer photophysikalischen und elektrochemischen Eigenschaften, wobei in dieser Arbeit mithilfe einer chemischen Reaktion eine gezielte Einstellung dieser Eigenschaften gezeigt werden konnte. Metallkomplexe mit solchen charakteristischen, leicht einstellbaren photophysikalischen sowie elektrochemischen Eigenschaften sind geeignete Sensor- und Elektronen-Shuttle-Molek{\"u}le besonders f{\"u}r bioanalytische Einsatzgebiete. Zudem k{\"o}nnten die vielen Einstellm{\"o}glichkeiten der elektronischen Struktur dieser Komplexe sehr interessant f{\"u}r katalytische Anwendungen sein.},
  language  = {de}
}
@phdthesis{Boroudjerdi2005,
  author    = {Boroudjerdi, Hoda},
  title     = {Charged polymer-macroion complexes},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-6282},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {This work explores the equilibrium structure and thermodynamic phase behavior of complexes formed by charged polymer chains (polyelectrolytes) and oppositely charged spheres (macroions). Polyelectrolyte-macroion complexes form a common pattern in soft-matter physics, chemistry and biology, and enter in numerous technological applications as well. From a fundamental point of view, such complexes are interesting in that they combine the subtle interplay between electrostatic interactions and elastic as well as entropic effects due to conformational changes of the polymer chain, giving rise to a wide range of structural properties. This forms the central theme of theoretical studies presented in this thesis, which concentrate on a number of different problems involving strongly coupled complexes, i.e. complexes that are characterized by a large adsorption energy and small chain fluctuations. In the first part, a global analysis of the structural phase behavior of a single polyelectrolyte-macroion complex is presented based on a dimensionless representation, yielding results that cover a wide range of realistic system parameters. Emphasize is made on the interplay between the effects due to the polyelectrolytes chain length, salt concentration and the macroion charge as well as the mechanical chain persistence length. The results are summarized into generic phase diagrams characterizing the wrapping-dewrapping behavior of a polyelectrolyte chain on a macroion. A fully wrapped chain state is typically obtained at intermediate salt concentrations and chain lengths, where the amount of polyelectrolyte charge adsorbed on the macroion typically exceeds the bare macroion charge leading thus to a highly overcharged complex. Perhaps the most striking features occur when a single long polyelectrolyte chain is complexed with many oppositely charged spheres. In biology, such complexes form between DNA (which carries the cell's genetic information) and small oppositely charged histone proteins serving as an efficient mechanism for packing a huge amount of DNA into the micron-size cell nucleus in eucaryotic cells. The resultant complex fiber, known as the chromatin fiber, appears with a diameter of 30~nm under physiological conditions. Recent experiments indicate a zig-zag spatial arrangement for individual DNA-histone complexes (nucleosome core particles) along the chromatin fiber. A numerical method is introduced in this thesis based on a simple generic chain-sphere cell model that enables one to investigate the mechanism of fiber formation on a systematic level by incorporating electrostatic and elastic contributions. As will be shown, stable complex fibers exhibit an impressive variety of structures including zig-zag, solenoidal and beads-on-a-string patterns, depending on system parameters such as salt concentration, sphere charge as well as the chain contour length (per sphere). The present results predict fibers of compact zig-zag structure within the physiologically relevant regime with a diameter of about 30~nm, when DNA-histone parameters are adopted. In the next part, a numerical method is developed in order to investigate the role of thermal fluctuations on the structure and thermodynamic phase behavior of polyelectrolyte-macroion complexes. This is based on a saddle-point approximation, which allows to describe the experimentally observed reaction (or complexation) equilibrium in a dilute solution of polyelectrolytes and macroions on a systematic level. This equilibrium is determined by the entropy loss a single polyelectrolyte chain suffers as it binds to an oppositely charged macroion. This latter quantity can be calculated from the spectrum of polyelectrolyte fluctuations around a macroion, which is determined by means of a normal-mode analysis. Thereby, a stability phase diagram is obtained, which exhibits qualitative agreement with experimental findings. At elevated complex concentrations, one needs to account for the inter-complex interactions as well. It will be shown that at small separations, complexes undergo structural changes in such a way that positive patches from one complex match up with negative patches on the other. Furthermore, one of the polyelectrolyte chains may bridge between the two complexes. These mechanisms lead to a strong inter-complex attraction. As a result, the second virial coefficient associated with the inter-complex interaction becomes negative at intermediate salt concentrations in qualitative agreement with recent experiments on solutions of nucleosome core particles.},
  subject      = {Biopolymere},
  language  = {en}
}