Atoms change their optical properties drastically when combined into molecules or crystals. This becomes evident when comparing isolated carbon atoms with their solid-state polymorphs graphite and diamond. Plasmonic meta-surfaces adopt this concept to design the optical properties of thin films at will. In analogy to natural materials, the optical response of a meta-surface is dictated by the arrangement and plasmonic coupling (hybridization) of sub-wavelength metallic objects, so-called meta-atoms, rather than by the individual components. Although traditional direct writing approaches offer a high degree of freedom in design of nanostructures, reconfiguration of meta-atoms is usually limited. Especially their spatial rearrangement remains a huge challenge. Postfabrication tunability, however, would be crucial to advance device miniaturization and optical computing, by introducing dynamically tunable optics and optical switches. This thesis investigates colloidal assembly as a cost-efficient approach to fabricate meta-surfaces on cm²-areas whose optical properties can be tuned by geometrical reconfiguration. Hydrodynamic fields and topographical templates guide the deposition of colloidal nanoparticles with precise orientational and/or positional control. In the course of this work, the level of particle assembly complexity is successively increased to realize 1-, 2-, and 3-dimensional (1D, 2D, 3D) plasmonic assemblies. Strongly correlated with assembly geometry, different aspects of light are controllable. (I) 1D alignment of silver nanowires (AgNWs) produces differential transmission for linear polarization states (linear dichroism). (II) Single particles in a 2D square array interact coherently to produce a sharp, so-called surface lattice resonance (SLR). This effect confines strong electromagnetic fields in the lattice plane, which is promising for plasmonic lasing. (III) 3D chiral, cross-stacked particle chains control the transmission of circular polarization states (circular dichroism, CD). The unique advantages of colloidal assembly are demonstrated. (I) Spray coating allows rapid deposition of oriented AgNWs over large areas and is compatible with roll-to-roll processing. Employing wrinkle-structured receiver substrates, gradients of continuously varying linear dichroism are feasible in a single step. (II) Capillary assembly is able to realize ~1 nm inter-particle spacing, which is not achievable by conventional top-down lithographical methods. The small spacing enhances inter-particle plasmon coupling and boosts CD in cross-stacked, chiral particle chains, as presented in this thesis. (III) Such hierarchical and restackable, chiral structures make large volumes of superchiral fields accessible for ultrasensitive, enantioselective detection of analytes. This is in vast contrast to stacked nanobars produced via lithography where the most pronounced fields in the inter-layer gap are blocked by the presence of spacing layers. A central focus of this thesis is the postfabrication reconfiguration of the systems presented. This in-situ tunability is realized by elastic and reversibly stackable templates. (I) Uniaxial, mechanical strain converts the 2D square lattice into a rectangular one. This splits the SLR into two polarization-dependent modes whose resonance position is shifted reversibly when load is applied. (II) The cross-stacked, chiral particle chains are restackable. This allows adjustment of the stacking angle to tune CD magnitude and sign. (III) Reversible compression of this chiral stack induces a bending of the chains to shift the spectral position of CD modes. In a proof of concept, locally varying compression is shown to create a gradient of CD response as important step towards on-chip CD spectroscopy. Overall, this thesis (I) tests the limits of colloidal assembly by going from single-particle arrays to complex 3D arrangements; (II) explores geometrical reconfiguration of these plasmonic nanostructures to tune pronounced optical effects. The strategies presented herein can be extended to other colloidal particle shapes and materials. Moreover, the concepts of restackable meta-surfaces and local compression for tuning optical response open an intriguing playground and might inspire top-down approaches as well. / Atome ändern ihre optischen Eigenschaften drastisch, wenn sie sich zu Molekülen oder Kristallen vereinigen. Dies wird deutlich, wenn man isolierte Kohlenstoffatome mit ihren Festkörperpolymorphen Graphit und Diamant vergleicht. Plasmonische Meta-Oberflächen übernehmen dieses Konzept, um die optischen Eigenschaften dünner Schichten nach Belieben einzustellen. In Analogie zu natürlichen Materialien wird die optische Antwort einer Meta-Oberfläche durch die Anordnung und plasmonische Kopplung (Hybridisierung) metallischer Mikro- und Nano-Objekte, den sogenannten Meta-Atomen, bestimmt und kann sich stark von den Eigenschaften der Einzelkomponenten unterscheiden. Obwohl traditionelle Direktschreibverfahren ein hohes Maß an Gestaltungsfreiheit in der Nanostrukturierung bieten, ist die Rekonfiguration von Meta-Atomen in der Regel begrenzt. Vor allem ihre räumliche Neuordnung bleibt eine große Herausforderung. Eine Durchstimmbarkeit auch nach der Herstellung zu gewährleisten wäre jedoch entscheidend, um die Miniaturisierung von Geräten und die Realisierung optischer Computer—durch die Einführung dynamisch durchstimmbarer optischer Bauteile und optischer Schalter—voranzutreiben. Diese Dissertation untersucht kolloidale Assemblierung als kostengünstigen Ansatz zur Herstellung von Meta-Oberflächen im cm²-Maßstab, deren optische Eigenschaften durch geometrische Rekonfiguration durchgestimmt werden können. Hydrodynamische Felder und topographische Template steuern die Ablagerung kolloidaler Nanopartikel mit präziser Orientierungs- und/oder Positionskontrolle. Im Verlauf dieser Arbeit wird die Komplexität der Partikelanordnung sukzessive erhöht, um 1-, 2- und 3-dimensionale (1D, 2D, 3D), plasmonische Anordnungen zu realisieren. Eng verbunden mit der Anordnungsgeometrie können verschiedene Aspekte des Lichts gesteuert werden. (I) Die 1D-Ausrichtung von Silbernanodrähten ruft unterschiedliche Transmission für lineare Polarisationszustände hervor (linearer Dichroismus). (II) Einzelpartikel in einem quadratischen 2D-Kristall wechselwirken kohärent, was eine scharfe, sogenannte Oberflächengitterresonanz (surface lattice resonance) erzeugt. Dieser Effekt konzentriert starke elektromagnetische Felder in der Gitterebene, was ihn für plasmonische Laser interessant macht. (III) 3D-chirale, über Kreuz geschichtete Partikelketten beeinflussen die Transmission zirkularer Polarisationszustände (zirkularer Dichroismus). Die einzigartigen Vorzüge der kolloidalen Assemblierung werden aufgezeigt. (I) Die Sprühbeschichtung ermöglicht eine rasche Abscheidung orientierter Silbernanodrähte auf großen Flächen und lässt sich mit kontinuierlicher Fertigung (Rolle-zu-Rolle) verbinden. Mit Hilfe faltenstrukturierter Substrate können Gradienten mit kontinuierlich variierendem Lineardichroismus in einem einzigen Schritt erzeugt werden. (II) Partikelanordnung mittels Kapillarkräften ermöglicht Partikelabstände von ~1 nm, was mit herkömmlichen, lithographischen Methoden nicht erreichbar ist. Dieser geringe Abstand verbessert die Plasmonenkopplung zwischen den Partikeln und verstärkt den Zirkulardichroismus in gekreuzten, chiralen Partikelketten, wie in dieser Arbeit vorgestellt wird. (III) Solche hierarchischen und wiederholt stapelbaren, chiralen Strukturen machen große Volumina an superchiralen Feldern für Analytmoleküle zugänglich, was deren ultrasensitive, enantioselektive Detektion ermöglicht. Dies steht in starkem Gegensatz zu gestapelten, lithographisch hergestellten Nanostäbchen, bei denen die stärksten Felder im Zwischenschichtspalt durch die Anwesenheit von Abstandsschichten versperrt bleiben. Ein zentrales Thema dieser Arbeit ist die Rekonfiguration der vorgestellten Systeme im Anschluss an deren Fertigung. Diese in-situ-Durchstimmbarkeit wird durch elastische und reversibel stapelbare Template realisiert. (I) Mechanische Deformation entlang einer Achse überführt den quadratischen 2D-Kristall in einen rechteckigen. Dadurch wird die Oberflächengitterresonanz in zwei polarisationsabhängige Moden aufgespalten, deren Resonanzposition unter Krafteinwirkung reversibel verschoben wird. (II) Die über Kreuz gestapelten, chiralen Partikelketten sind wiederholt stapelbar. Dies ermöglicht die Anpassung des Stapelwinkels, um die Stärke und das Vorzeichen des Zirkulardichroismus einzustellen. (III) Reversible Kompression dieses chiralen Stapels verursacht ein Verbiegen der Ketten und verschiebt so die spektrale Position der zirkulardichroitischen Moden. In einer Machbarkeitsstudie konnte gezeigt werden, dass lokal variierende Kompression einen Gradienten des Zirkulardichroismus hervorruft. Dies stellt einen wichtigen Schritt in Richtung Ein-Chip-Spektroskopie dar. Diese Arbeit (I) lotet die Grenzen der kolloidalen Assemblierung aus, indem sie von Einzelpartikel-Anordnungen zu komplexen 3D-Arrangements übergeht; (II) untersucht die geometrische Rekonfiguration dieser plasmonischen Nanostrukturen, um ausgeprägte optische Effekte zu modulieren. Die hier vorgestellten Strategien können auf andere kolloidale Partikelformen und materialien übertragen werden. Darüber hinaus bereiten die Konzepte wiederholt stapelbarer Meta-Oberflächen und der lokalen Kompression zum Einstellen der optischen Eigenschaften eine faszinierende Spielwiese. Auch der Top-Down-Fertigung könnten diese Ansätze als Blaupause dienen.

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Chemotherapy works by killing fast dividing cells. Unfortunately, these drugs are not specific to cancer tissue and can damage normal cells. Chemotherapy is like taking poison and hoping it kills the cancer cells before it kills you. As an alternative, many researchers have investigated the use of antigene therapy to selectively target cancer causing genes to avoid off target effects. Although promising, the theory is limited by the stability of the triplex structure. Here, we report the discovery of potent triplex binding ligands derived from the natural product quercetin. Chemical derivatives of 5-substituted 3, 3’, 4’, 7-tetramethoxyquercetin derivatives were characterized using several biophysical methods: thermal denaturation monitored by UV, circular dichroism, viscometry, differential scanning calorimetry, and isothermal titration calorimetry. The data revealed that these derivatives specifically stabilize triplex DNA and do not influence the stability of duplex DNA, triple RNA, or duplex RNA. Structurally, the amino containing side chains at the 5-position and the linker length are critical for the observed binding affinity and specificity. Two derivatives, 5 and 7, are comparable (if not better) to the triplex groove binder Neomycin. Our data confirm the binding mode as enthalpically driven intercalation. Piperidine or pyrrolidine 5-substituted 3, 3’, 4’, 7-tetramethoxyquercetin derivatives with a three-carbon linker are the lead compounds for development as a potential antigene enhancer.

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Bacterial DNA replication can stall at DNA lesions, leading to cell death if the damage fails to be repaired. To circumvent this, bacteria possess a mechanism called translesion DNA synthesis (TLS) to allow DNA damage bypass. The ImuABC TLS mutasome comprises the RecA domain-containing protein ImuA, the inactive polymerase ImuB, and the error-prone polymerase ImuC. ImuA and ImuB are necessary for the mutational function of ImuC that can lead to antimicrobial resistance (AMR) as seen in high-priority pathogens Pseudomonas aeruginosa and Mycobacterium tuberculosis. Understanding how ImuA and ImuB contribute to this function can lead to new targets for antimicrobial development. This research aims to discover the molecular functions of ImuA and ImuB homologs from Myxococcus xanthus through structural modelling and biochemical analyses. ImuA was discovered to be an ATPase whose activity is enhanced by DNA. Based on predicted structural models of the ATPase active site, I identified the critical residues needed for ATP hydrolysis, and found that the ImuA C-terminus regulates ATPase activity. Further, ImuA and ImuBNΔ34 (a soluble truncation of ImuB) display a preference for longer single-stranded DNA and overhang DNA substrates, and their affinity for DNA was quantified in vitro. To better understand how ImuA and ImuB assemble in the TLS mutasome, bacterial two-hybrid assays determined that ImuA and ImuB can self-interact and bind one another. Mass photometry revealed that ImuA is a monomer and ImuBNΔ34 is a trimer in vitro. ImuA and ImuBNΔ34 binding affinity was quantified in vitro at 1.69 μM ± 0.21 by microscale thermophoresis, and removal of the ImuA C-terminus weakens this interaction. Lastly, ImuA and ImuBNΔ34 secondary structures were quantified using circular dichroism spectroscopy, and ImuA was modified to enable crystallization for future structural studies. Together, this research provides a better understanding of ImuABC-mediated TLS, potentially leading to novel antibiotics to reduce the clinical burden of AMR. / Thesis / Master of Science (MSc) / The antimicrobial resistance (AMR) crisis is fueled by the emergence of multi-drug resistant microbes, posing a major threat to global health and disease treatment. Bacteria can develop resistance to antibiotics through mutations in the genome. When the genome becomes damaged, bacteria can acquire these mutations by an error-prone replication mechanism called translesion DNA synthesis (TLS). In some bacteria, TLS involves a specialized enzyme complex, consisting of proteins ImuA, ImuB and ImuC, allowing replication past bulky DNA damage and lesions. The goal of this thesis is to investigate how the ImuA and ImuB proteins contribute to the functioning of this mistake-making machinery. I used biochemical and biophysical methods to identify ImuA and ImuB interactions with each other and themselves. I discovered that ImuA is an enzyme that uses energy to enhance its binding to DNA, and determined the specific amino acids involved in this function.

In dieser Arbeit werden systematisch die bisher unerforschten grundlegenden physikalischen und chemischen Eigenschaften von DNA-Origami untersucht, die die Stabilität dieser aus doppelsträngiger DNA aufgebauten nanoskopischen Suprastrukturen bestimmen. In Analogie zu den zahlreichen Studien, die sich mit der Stabilität von Proteinen durch kontrollierte Denaturierung beschäftigen, spielen auch in dieser Arbeit die Denaturierungsbedingungen eine zentrale Rolle. Unter Verwendung von Guanidinium (Gdm+) als teilweise DNA-stabilisierendes, aber auch potentiell denaturierendes Kation steht dessen Wirkung auf DNA-Origami-Dreiecke im Mittelpunkt der Untersuchungen, wobei insbesondere die unerwartete Modulation der nanoskopischen Schädigung von DNA-Origami durch die begleitenden Gegenanionen zu Gdm+ im Vordergrund steht. Die Experimente zielen darauf ab, atomistische, molekulare, nanoskopische und thermodynamische Eigenschaften von DNA-Origami zu korrelieren und zu klären, wie diese vom Design des DNA-Origami selbst abhängen können. Die Ergebnisse zeigen einen unerwarteten Zusammenhang zwischen den spezifischen Gegenanionen des Denaturierungsmittels und der Stabilität der DNA-Origami-Dreiecke: Sulfat wirkt stabilisierend, während Chlorid die Superstruktur bereits unterhalb der globalen Schmelztemperatur destabilisiert. Statistische Analysen von Rasterkraftmikroskop (AFM)-Bildern und Zirkulardichroismus (CD)-Spektren zeigen Strukturübergänge auf nano-skopischer bzw. molekularer Ebene. Werden diese Techniken mit thermischer Denaturierung in Gegenwart von schwacher bis starker chemischer Denaturierung kombiniert, so zeigt sich, dass Änderungen der Wärmekapazität (ΔCp) während der strukturellen Veränderungen der DNA-Originale eine Schlüsselrolle bei der Bestimmung ihrer Empfindlichkeit gegenüber Temperatur und Denaturierungsmitteln spielen. Die Daten deuten darauf hin, dass Wasser auf apolaren DNA-Origami-Oberflächen der molekulare Ursprung der abgeleiteten Wärme-kapazitätsänderungen ist. Diese Hypothese wird durch Molekulardynamik-Simulationen (MD) unterstützt, die die Modulation von ΔCp durch die Hydratationshüllen der Anionen zeigen. Ihr unterschiedliches Potential, stabile Ionenpaare mit Gdm+ in konzentrierten Salzlösungen zu bilden, kann die experimentell beobachteten Variationen der strukturellen Stabilität erklären. Die Kopplung von strukturellen Übergängen an ΔCp wird somit als Schlüsselfaktor für die Destabilisierung von DNA-Origami sowohl bei höheren als auch bei niedrigeren Temperaturen identifiziert. Darüber hinaus weisen DNA-Origami nicht nur diese Eigenschaft auf, sondern ermöglichen auch die Beobachtung von kalten Denaturierungsprozessen auf nanoskopischer Ebene, bei denen kälteinduzierte Spannungen innerhalb der Superstruktur bei einem Bruch an vorherbestimmten lokalen Stellen freigesetzt werden, die in AFM-Bildern sichtbar sind. Dies ist die erste Beobachtung der kälteinduzierten Denaturierung von Nukleinsäuren bei Temperaturen über 0 °C sowie von DNA-basierten Superstrukturen. In dieser Arbeit wird die strukturelle Stabilität von sechs verschiedenen 2D- und 3D-DNA-Origami-Nanostrukturen in unterschiedlichen chemischen Umgebungen untersucht. Drei chaotrope Salze - Guanidiniumsulfat (Gdm2SO4), Guanidiniumchlorid (GdmCl) und Tetrapropylammoniumchlorid (TPACl) - werden als Denaturierungsmittel verwendet. Mittels Rasterkraftmikroskopie wird die Integrität der Nanostrukturen quantifiziert, wobei sich Gdm2SO4 als das schwächste und TPACl als das stärkste Denaturierungsmittel für DNA-Origami erweist, was sich auch in den Schmelztemperaturen widerspiegelt. Die Abhängigkeit der DNA-Origami-Stabilität von der Superstruktur wird besonders bei 3D-Nanostrukturen deutlich. Hier zeigen mechanisch flexible Designs sowohl in GdmCl als auch in TPACl eine höhere Stabilität als ihre starren Gegenstücke. Die Abhängigkeit der DNA-Origami-Stabilität von der Superstruktur wird besonders in 3D-Nanostrukturen deutlich, in denen mechanisch flexible Strukturen sowohl in GdmCl als auch in TPACl eine höhere Stabilität aufweisen als ihre steifen Gegenstücke. Dies begünstigt die Bildung von intramolekularen Verformungen, die sich entweder in 'weichen' Architekturen über die gesamte Superstruktur verteilen oder in ansonsten 'steifen' Strukturen in den weniger stabilen Regionen konzentrieren.:Table of contents Questions addressed in this thesis .................................................................................... I Abstract ................................................................................................................................ I Englisch .................................................................................................................................................. I Deutsch .................................................................................................................................................. II Acronyms ........................................................................................................................... III Substances .......................................................................................................................................... IV Physical and Chemical abbreviations ............................................................................................... IV Mathematical abbreviations ................................................................................................................ V 1 Introduction ................................................................................................................. 1 1.1 Deoxyribonucleic acid ................................................................................................................. 1 1.1.1 The structure of DNA ............................................................................................................ 1 1.1.2 Hydrogen bonds .................................................................................................................... 1 1.1.3 Base stacking ........................................................................................................................ 2 1.1.4 Water DNA interactions: A complex dance of stability and dynamics .................................. 5 1.1.5 The effect of ionic strength on DNA conformation ................................................................ 9 1.1.6 Conformational changes ....................................................................................................... 9 1.1.7 Forms of DNA ..................................................................................................................... 10 1.1.8 The role of apolar groups in DNA unfolding ........................................................................ 13 1.1.9 Energetics of DNA structural transitions ............................................................................. 14 1.1.10 Melting temperature ............................................................................................................ 15 1.2 Hofmeister series ....................................................................................................................... 17 1.2.1 Probing the Hofmeister series: Salt effects biomolecules ................................................... 17 1.2.2 Specific ion effects in electrolyte solutions .......................................................................... 19 1.3 DNA nanostructures................................................................................................................... 20 1.3.1 DNA origami ........................................................................................................................ 22 1.3.2 Challenges in DNA origami stability .................................................................................... 26 1.3.3 DNA origami in single molecule studies .............................................................................. 27 1.4 Circular dichroism ...................................................................................................................... 28 1.4.1 Circular dichroism spectroscopy for analyzing DNA conformations ................................... 30 1.4.2 Wavelength-dependent spectroscopic signatures of DNA conformation ........................... 32 1.5 Atomic force microscopy .......................................................................................................... 34 1.6 2D correlation spectroscopy ..................................................................................................... 36 1.6.1 2D correlation spectroscopy: Synchronous and asynchronous spectra analysis ............... 39 1.6.2 Perturbation-correlation moving-window 2D correlation spectroscopy ............................... 40 1.7 Multivariate analysis of spectral data using PCA and ITTFA ................................................ 41 1.8 Cold denaturation ....................................................................................................................... 42 2 Results and Discussion ............................................................................................ 44 2.1 Cold denaturation of the Rothemund DNA origami triangle .................................................. 45 2.2 Heat denaturation of the Rothemund DNA origami triangle .................................................. 50 2.2.1 Investigations by atomic force microscopy ......................................................................... 51 2.2.2 Circular dichroism spectroscopy and thermodynamic modelling ........................................ 56 2.2.3 Divergent effects of Cl- and SO42- on DNA origami stability ................................................ 62 2.3 Magnesium concentration modulation of DNA Origami heat denaturation ......................... 65 2.4 Assessing DNA origami stability in different chaotropic environments .............................. 66 2.4.1 DNA origami integrity influenced by Gdm2SO4 ................................................................... 67 2.4.2 DNA origami integrity influenced by GdmCl ........................................................................ 73 2.4.3 DNA origami integrity influenced by TPACl ........................................................................ 75 2.4.4 Quantitative comparison ..................................................................................................... 77 3 Critics ......................................................................................................................... 78 4 Conclusion ................................................................................................................. 79 5 Outlook ...................................................................................................................... 81 6 Material and Methods ................................................................................................ 82 6.1 DNA origami synthesis .............................................................................................................. 82 6.2 Sample preparation and AFM imaging ..................................................................................... 82 6.2.1 Anion-specific structure and stability of guanidinium-bound DNA origami & Cold denaturation of DNA origami nanostructures ...................................................................... 82 6.2.2 Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants ........................................................................................................ 83 6.2.3 Cold denaturation of DNA origami nanostructures ............................................................. 83 6.3 CD spectroscopy and analysis ................................................................................................. 84 6.3.1 Anion-specific structure and stability of guanidinium-bound DNA origami ......................... 84 6.3.2 Pre-treatment of the CD data and calculation of melting temperatures .............................. 84 6.3.3 Cold denaturation of DNA origami nanostructures ............................................................. 84 6.3.4 Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants ........................................................................................................ 84 6.4 Principal component analysis and iterative target test factor analysis ............................... 85 6.5 Thermodynamic modelling ........................................................................................................ 85 6.6 Molecular dynamics modelling ................................................................................................. 85 Appendix ........................................................................................................................... 88 Acknowledgment ............................................................................................................ 100 Bibliography .................................................................................................................... 101 List of Figures ................................................................................................................. 116 List of Tables ................................................................................................................... 118 Declaration of independence – Selbstständigkeitserklärung ...................................... 119 / This thesis undertakes the systematic study of hitherto unexplored fundamental physical and chemical properties of DNA origami that determine the stability of these designed nanoscopic superstructural assemblies of double-stranded DNA. In analogy to the vast number of studies addressing protein stability by controlled denaturation, denaturing conditions play a central role in this thesis as well. Using guanidinium (Gdm+) as a partly DNA-stabilizing but also potentially denaturing cation, its effect on DNA origami triangles is central to the study which particularly addressed the unexpected modulation of nanoscopic damage of DNA origami by the accompanying counter-anions to Gdm+. The experiments aim at correlating atomistic, molecular, nanoscopic and thermodynamic properties of DNA origami and at elucidating how these may depend on the DNA origami design itself. The results demonstrate an unexpected relationship between the specific counter-anions of the denaturant and the stability of DNA origami triangles: sulphate exhibits stabilizing effects and chloride induces destabilization of the superstructure already below the global melting temperature. Statistical analyses of both atomic force microscopy (AFM) images and circular dichroism (CD) spectra reveal structural transitions at the nanoscopic and molecular level, respectively. Combining these techniques with thermal denaturation in the presence of mild to strong chemical denaturation, changes in heat capacity (ΔCp) during DNA origami structural changes are shown to play the key role in determining their sensitivity to temperature and denaturants. The data suggest that water at apolar DNA origami surfaces is the molecular origin of the derived heat capacity changes. This hypothesis is substantiated by Molecular Dynamics (MD) simulations which shed light on the modulation of ΔCp by the hydration shells of anions. Their different potential to form stable ion pairs with Gdm+ in concentrated salt solutions can explain the experimentally observed variations of structural stability. The coupling of structural transitions to ΔCp is thus identified as a key factor in the destabilization of DNA origami at both elevated and lowered temperatures. Furthermore, DNA origami not only exhibit this property, but also enable the observation of cold denaturation processes at the nanoscopic level, where cold-induced strain within the superstructure is released upon breakage at predisposed local sites, visible in AFM images. This is the first observation of cold-induced denaturation of nucleic acids at temperatures above 0 °C, as well of DNA-based superstructures. Extending the scope, the work evaluates the structural stability of six different 2D and 3D DNA origami nanostructures in different chemical environments. Three chaotropic salts - guanidinium sulfate (Gdm2SO4), guanidinium chloride (GdmCl), and tetrapropylammonium chloride (TPACl) - are used as denaturants. Atomic force microscopy quantifies the nanostructural integrity, revealing Gdm2SO4 as the weakest and TPACl as the strongest DNA origami denaturant, which is also reflected in the melting temperatures. The dependence of DNA origami stability on its superstructure is particularly evident in 3D nanostructures, where mechanically flexible designs exhibit higher stability in both GdmCl and TPACl than rigid counterparts. This supports the buildup of intramolecular strain, which becomes either partitioned among the entire superstructure in “soft” architectures or accumulates at the least stable regions in otherwise “rigid” designs.:Table of contents Questions addressed in this thesis .................................................................................... I Abstract ................................................................................................................................ I Englisch .................................................................................................................................................. I Deutsch .................................................................................................................................................. II Acronyms ........................................................................................................................... III Substances .......................................................................................................................................... IV Physical and Chemical abbreviations ............................................................................................... IV Mathematical abbreviations ................................................................................................................ V 1 Introduction ................................................................................................................. 1 1.1 Deoxyribonucleic acid ................................................................................................................. 1 1.1.1 The structure of DNA ............................................................................................................ 1 1.1.2 Hydrogen bonds .................................................................................................................... 1 1.1.3 Base stacking ........................................................................................................................ 2 1.1.4 Water DNA interactions: A complex dance of stability and dynamics .................................. 5 1.1.5 The effect of ionic strength on DNA conformation ................................................................ 9 1.1.6 Conformational changes ....................................................................................................... 9 1.1.7 Forms of DNA ..................................................................................................................... 10 1.1.8 The role of apolar groups in DNA unfolding ........................................................................ 13 1.1.9 Energetics of DNA structural transitions ............................................................................. 14 1.1.10 Melting temperature ............................................................................................................ 15 1.2 Hofmeister series ....................................................................................................................... 17 1.2.1 Probing the Hofmeister series: Salt effects biomolecules ................................................... 17 1.2.2 Specific ion effects in electrolyte solutions .......................................................................... 19 1.3 DNA nanostructures................................................................................................................... 20 1.3.1 DNA origami ........................................................................................................................ 22 1.3.2 Challenges in DNA origami stability .................................................................................... 26 1.3.3 DNA origami in single molecule studies .............................................................................. 27 1.4 Circular dichroism ...................................................................................................................... 28 1.4.1 Circular dichroism spectroscopy for analyzing DNA conformations ................................... 30 1.4.2 Wavelength-dependent spectroscopic signatures of DNA conformation ........................... 32 1.5 Atomic force microscopy .......................................................................................................... 34 1.6 2D correlation spectroscopy ..................................................................................................... 36 1.6.1 2D correlation spectroscopy: Synchronous and asynchronous spectra analysis ............... 39 1.6.2 Perturbation-correlation moving-window 2D correlation spectroscopy ............................... 40 1.7 Multivariate analysis of spectral data using PCA and ITTFA ................................................ 41 1.8 Cold denaturation ....................................................................................................................... 42 2 Results and Discussion ............................................................................................ 44 2.1 Cold denaturation of the Rothemund DNA origami triangle .................................................. 45 2.2 Heat denaturation of the Rothemund DNA origami triangle .................................................. 50 2.2.1 Investigations by atomic force microscopy ......................................................................... 51 2.2.2 Circular dichroism spectroscopy and thermodynamic modelling ........................................ 56 2.2.3 Divergent effects of Cl- and SO42- on DNA origami stability ................................................ 62 2.3 Magnesium concentration modulation of DNA Origami heat denaturation ......................... 65 2.4 Assessing DNA origami stability in different chaotropic environments .............................. 66 2.4.1 DNA origami integrity influenced by Gdm2SO4 ................................................................... 67 2.4.2 DNA origami integrity influenced by GdmCl ........................................................................ 73 2.4.3 DNA origami integrity influenced by TPACl ........................................................................ 75 2.4.4 Quantitative comparison ..................................................................................................... 77 3 Critics ......................................................................................................................... 78 4 Conclusion ................................................................................................................. 79 5 Outlook ...................................................................................................................... 81 6 Material and Methods ................................................................................................ 82 6.1 DNA origami synthesis .............................................................................................................. 82 6.2 Sample preparation and AFM imaging ..................................................................................... 82 6.2.1 Anion-specific structure and stability of guanidinium-bound DNA origami & Cold denaturation of DNA origami nanostructures ...................................................................... 82 6.2.2 Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants ........................................................................................................ 83 6.2.3 Cold denaturation of DNA origami nanostructures ............................................................. 83 6.3 CD spectroscopy and analysis ................................................................................................. 84 6.3.1 Anion-specific structure and stability of guanidinium-bound DNA origami ......................... 84 6.3.2 Pre-treatment of the CD data and calculation of melting temperatures .............................. 84 6.3.3 Cold denaturation of DNA origami nanostructures ............................................................. 84 6.3.4 Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants ........................................................................................................ 84 6.4 Principal component analysis and iterative target test factor analysis ............................... 85 6.5 Thermodynamic modelling ........................................................................................................ 85 6.6 Molecular dynamics modelling ................................................................................................. 85 Appendix ........................................................................................................................... 88 Acknowledgment ............................................................................................................ 100 Bibliography .................................................................................................................... 101 List of Figures ................................................................................................................. 116 List of Tables ................................................................................................................... 118 Declaration of independence – Selbstständigkeitserklärung ...................................... 119

No description available.