@phdthesis{Neitz2024,
  author    = {Neitz, Hermann},
  title     = {Hydrophobic recognition motifs in functionalized DNA},
  doi       = {10.25972/OPUS-34838},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-348382},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {In w{\"a}ssriger Umgebung spielen hydrophobe Wechselwirkungen eine wichtige Rolle f{\"u}r die DNA. Die Einf{\"u}hrung von Modifikationen, die auf hydrophoben aromatischen Einheiten basieren, kann die Erkennung und Reaktivit{\"a}t von funktionellen Gruppen in der DNA steuern. Modifikationen k{\"o}nnen durch ein k{\"u}nstliches R{\"u}ckgrat oder in Form einer Erweiterung der Nukleobasen eingebracht werden und so zu zus{\"a}tzlichen Eigenschaften der DNA f{\"u}hren. Diese Dissertation befasst sich mit der Verwendung von hydrophoben Einheiten zur Funktionalisierung von DNA. Im ersten Teil der Arbeit wurde das Tolanmotiv (Diphenylacetylen) in Kombination mit dem acyclischen R{\"u}ckgrat von GNA und BuNA verwendet, um Erkennungseinheiten im DNA-Kontext zu erzeugen. Die gezielte Fluorierung der aromatischen Ringe des Tolan-Bausteins bildete die Grundlage f{\"u}r eine supramolekulare Sprache, die auf Aren-Fluoroaren-Wechselwirkungen basiert. Die spezifische Erkennung wurde mittels thermodynamischer, kinetischer und NMR-spektroskopischer Methoden untersucht. Im zweiten Teil der Arbeit wurden Desoxyuridin-Derivate mit einer hydrophoben aromatischen Modifikation hergestellt und in die DNA-Doppelhelix eingebaut. Die Bestrahlung mit UV-Licht f{\"u}hrte zu einer [2+2]-Cycloaddition zwischen zwei modifizierten Nukleosiden in der DNA. Das Reaktionsprodukt wurde strukturell charakterisiert und die Reaktion in verschiedenen biochemischen und nanotechnologischen DNA-Anwendungen eingesetzt.},
  subject      = {Supramolekulare Chemie},
  language  = {en}
}
@phdthesis{Siewert2021,
  author    = {Siewert, Aaron},
  title     = {Nucleotide analogs as rigid spin labels for DNA and RNA},
  doi       = {10.25972/OPUS-24765},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-247657},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Nucleic acids are one of the important classes of biomolecules together with carbohydrates, proteins and lipids. Both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are most well known for their respective roles in the storage and expression of genetic information. Over the course of the last decades, nucleic acids with a variety of other functions have been discovered in biological organisms or created artificially. Examples of these functional nucleic acids are riboswitches, aptamers and ribozymes. In order to gain information regarding their function, several analytical methods can be used. Electron paramagnetic resonance (EPR) spectroscopy is one of several techniques which can be used to study nucleic acid structure and dynamics. However, EPR spectroscopy requires unpaired electrons and because nucleic acids themselves are not paramagnetic, the incorporation of spin labels which carry a radical is necessary. Here, three new spin labels for the analysis of nucleic acids by EPR spectroscopy are presented. All of them share two important design features. First, the paramagnetic center is located at a nitroxide, flanked by ethyl groups to prevent nitroxide degradation, for example during solid phase synthesis. Furthermore, they were designed with rigidity as an important quality, in order to be useful for applications like pulsed electron double resonance (PELDOR) spectroscopy, where independent motion of the spin labels relative to the macromolecule has a noticeable negative effect on the precision of the measurements. Benzi-spin is a spin label which differs from most previous examples of rigid spin labels in that rather than being based on a canonical nucleoside, with a specific base pairing partner, it is supposed to be a universal nucleoside which is sufficiently rigid for EPR measurements when placed opposite to a number of different nucleosides. Benzi-spin was successfully incorporated into a 20 nt oligonucleotide and its base pairing behavior with seven different nucleosides was examined by UV/VIS thermal denaturation and continuous wave (CW) EPR experiments. The results show only minor differences between the different nucleosides, thus confirming the ability of benzi-spin to act as a universally applicable spin label. Lumi-spin is derived from lumichrome. It features a rigid scaffold, as well as a free 2'-hydroxy group, which should make it well suited for PELDOR experiments once it is incorporated into RNA oligonucleotides. E{\c{C}}r is based on the {\c{C}} family of spin labels, which contains the most well known rigid spin labels for nucleic acids to this day. It is essentially a version of E{\c{C}}m with a free 2'-hydroxy group. It was converted to triphosphate E{\c{C}}rTP and used for primer extension experiments to test the viability of enzymatic incorporation of rigid spin labels into oligonucleotides as an alternative to solid-phase synthesis. Incorporation into DNA by Therminator III DNA polymerase in both single-nucleotide and full-length primer extensions was achieved. All three of these spin labels represent further additions to the expanding toolbox of EPR spectroscopy on nucleic acids and might prove valuable for future research.},
  subject      = {Nucleins{\"a}uren},
  language  = {en}
}
@phdthesis{Gershberg2016,
  author    = {Gershberg, Jana},
  title     = {Self-assembled Perylene Bisimide Dimers and their Interaction with Double-stranded DNA},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-136725},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2016},
  abstract  = {The self-assembly of molecules based on π-π-interactions and hydrogen bonding is of significant importance in nature. These processes enable the formation of complex supramolecular structures with diverse functions. For the transfer of the concepts from nature to artificial supramolecular structures, a basic understanding of those processes is needed. For this purpose, π-conjugated aromatic molecules with an easy synthetic access are suitable as their functionalities can be changed effortless. Perylene bisimide (PBIs) dyes are attractive candidates since they fulfill these requirements owing to their tendency to self-assemble in solution due to their large aromatic π-surfaces. Furthermore, the changes of the optical properties (for instance absorption, emission or circular dichroism) of PBI dyes, caused by their self-assembly, are easy to study experimentally. Structural variations of PBI dyes including additional non-covalent interactions, such as hydro-gen bonding, enable to direct their self-assembly process. Thus, the formation of interesting su-pramolecular structures of PBI dyes could be realized, although, often of undefined size. The aim of this thesis was to develop strategies to restrict the aggregate size of PBI dyes. Therefore, de-fined structural features of PBI molecules were combined and a variation of external influences such as solvent and concentration included. Furthermore, DNA was utilized as a template for the limitation of the aggregate size of PBI dyes. Chapters 1 and 2 provide general information and describe examples from literature which are necessary to understand the following experimental work. The first chapter is based on the inter-actions of various molecules with DNA. Therefore, DNA is considered as a supramolecular biom-acromolecule containing specific structural and functional features to interact with small mole-cules. Afterwards, the main interaction modes of small molecules with DNA such as electrostatic interaction, intercalation and groove binding with corresponding examples are discussed. Among all techniques applied to study the interaction of ligands with DNA, UV/Vis absorption, fluores-cence and circular dichroism spectroscopy were described in detail. At the end of this chapter, examples of already pre-associated systems showing interactions with DNA are presented. The second chapter is focused on the determination and mathematic evaluation of the self-assembly processes. The simplest models such as monomer-dimer and isodesmic model are de-scribed and supplemented by examples. Furthermore, the simplest modification of the isodesmic model, the K2-K model, is presented. Additionally, experimental problems, which may arise dur-ing the investigations of the self-assembly processes, are addressed. For the description of the entire self-assembly process, a sufficiently large concentration range and an appropriate measure-ment method that is sensitive in this concentration range is necessary. Furthermore, the full transi-tion from the monomeric to the aggregated species has to be spectroscopically ascertainable. This enables an accurate mathematic evaluation of the self-assembly process and provides meaningful binding constants. The self-assembly pathway can be controlled by the variation of solvent, con-centration or temperature. However, this pathway can also be directed by a rational design of the molecular structure of the considered system. For example, a specific interplay of π-π-interactions and hydrogen bonding may promote isodesmic as well as cooperative growth into large struc-tures. The main focus of this thesis is to develop strategies to control the aggregate size of PBI dyes (Chapter 3). For this purpose, a PBI scaffold was designed which contains hydrogen bonding amide functions at the imide positions derived from the amino acid L-alanine and solubilizing side groups in the periphery (Figure 81). The variations of the residues R/R' range from didodecylox-yphenyl, didodecylphenyl, dioligo(ethylene glycol)phenyl to branched and linear alkyl chains. The most extensive study of the aggregation behavior was performed for the PBI dye 5. Concen-tration-dependent 1H NMR and UV/Vis absorption measurements clearly revealed the formation of dimers in chloroform. Further investigations by means of 2D NMR, VPO and ITC confirmed the exclusive presence of dimer aggregates of PBI 5 in the investigated concentration range. Mo-lecular modelling studies, supported by NMR and FT-IR experiments, provided structural reasons for the absence of further growth into larger aggregates. The specific combination of π-π interac-tions and hydrogen bonds between the NH groups of the amide groups and the carbonyl oxygen atoms of the PBI core are decisive for the formation of the discrete dimer stack (see Figure 82). The investigations of the aggregation behavior of PBIs 6-9 were less extensive but consistent with the results obtained for PBI 5. However, the determined binding constants vary over a considera-ble range of 1.1 x 102 M-1 (PBI 8) to 1.4 x 104 M-1 (PBI 5). These differences could be attributed to structural variations of the dyes. The electron-rich phenyl substituent promoted the aggregation tendency of PBIs 5-7 compared with 8 and 9 that carry only alkyl side chains. Thus, the π-π in-teractions of bay-unsubstituted PBI cores in combination with hydrogen bonding of the amide functions control the formation of discrete dimers of these PBI dyes. The variation of conditions, such as solvent, change the aggregation behavior of PBI dyes. In the solvents toluene and/or methylcyclohexane, anti-cooperative growth into larger aggregates of PBI 5 was observed (Chapter 4). The important feature of this self-assembly process is the absence of isosbestic points over the whole concentration range in the UV/Vis absorption measurements. The preference for the dimeric species of PBI 5 remained in both solvents as well as in mixtures of them, but upon increasing the concentration these dimers self-assemble into larger aggregates. An important feature of the self-assembly process is the preferred formation of even-numbered aggregates compared to the odd-numbered ones (see Figure 83). Although, the conventional K2-K model provides plausible binding constants, it is not capable to describe the aggregation behavior adequately, since it considers a continuous size distribution. The gradual aggregation process over dimers, tetramers, hexamers, etc. was therefore analyzed with a newly developed K2-K model for anti-cooperative supramolecular polymerization. By the global analysis of the UV/Vis absorption spectra a very good agreement between the experimental and simulated spectra, which were based on the new K2-K model, was obtained. Furthermore, the calculated UV/Vis absorption spectra of a dimer and an aggregate highlighted the most important structural differences. The absorption spectrum of the dimer still has a pronounced vibronic structure which gets lost in the spectrum of the aggregate. In another part of this work, a series of water soluble PBI dyes were described which contain similar PBI scaffolds as PBIs 5-8 (Chapter 5). These PBI dyes self-assemble into similar dimer aggregates in water due to their positively charged side chains causing electrostatic repulsion be-tween the molecules (see Figure 84). Here, however, the self-assembly behavior has not been studied thoroughly in water due to the similarities of already reported PBI dyes. Instead, the focus here is on the characterization of the interactions of these dyes with DNA/RNA. The comprehensive studies using thermal denaturation experiments showed the high stability of these PBI/polynucleotide complexes. The spermine-functionalized PBI dyes having six positive charges showed strong interactions with DNA/RNA which was expressed in a signif-icant increase of the melting temperatures of DNA/RNA (ΔTm values between 7 and > 35 ° C). The dioxa analogues containing only two positive charges had lower enhancement of the melting temperature of DNA/RNA (ΔTm values between 3 and 30 ° C). A similar trend has been observed in the fluorimetric titrations. The spermine-functionalized PBI dyes showed high binding con-stants (log Ks = 9.2 - 9.8), independently of the used polynucleotides. In contrast, the dioxa ana-logues displayed smaller binding constants (log Ks = 6.5 - 7.9) without any correlation between binding affinity and binding strength of the PBI dyes and the applied polynucleotides. The CD-spectroscopic measurements revealed significant differences in the binding properties of the dyes with DNA/RNA. They were dependent on the steric hindrance of the amino acid residues at the imide position and their configuration on one side and the grooves properties of ds-DNA/RNA on the other side. The spectroscopic results confirmed the formation of excitonically coupled PBI dimers in the minor groove of ds-DNA and the major groove of ds-RNA. Depending on the se-quence, the grooves of the polynucleotides provide different amount of space for embedding molecules. The guanine amino groups protrude into the minor groove of the polynucleotide poly(dG-dC)2 increasing the steric hindrance, which is not the case for poly(dA-dT)2. Molecular modeling studies showed that the PBI dimers penetrate deeper into the groove of poly(dA-dT)2 due to the absence of the steric hindrance, in comparison to the groove of poly(dG-dC)2 (see Figure 85).},
  subject      = {Perylentetracarbons{\"a}urederivate},
  language  = {en}
}