DNA Architectonics: Self-Assembly of Amphiphilic Oligonucleotides into Supramolecular Nanostructures

The first chapter aims at introducing topics related to the thesis. These include supramolecular polymers in aqueous medium, some structural aspects of deoxyribonucleic acid (DNA), the preparation of synthetic oligomers, the concept of aggregation-induced emission (AIE), and different approaches for the construction of DNA nanostructures. This introduction, with a focus on what has been reported previously in our research group, is followed by elucidating the aim of the thesis in chapter 2. The results of the experimental lab work are discussed in the subsequent chapters. In the third chapter, amphiphilic DNA conjugates exhibiting hydrophobic tetraphenylethylene (TPE) sticky ends at the 3’-ends are examined. Supramolecular assembly of such DNA duplexes results in two distinct vesicular morphologies – they either appear as prolate ellipsoids or spheres. The two different DNA architectures are characterized by their DNA duplex alignment within the supramolecular arrays. Only one type of DNA packing leads to the formation of DNA-addressable vesicular constructs. The self-assembly of 3’-/5’-end TPE-modified DNA duplexes into vesicular nanostructures are explored in chapter 4. The objective of this chapter is to investigate the influence of the TPE sticky ends and DNA sequence length on the self-assembly behavior of the duplexes. The fifth chapter is devoted to further functionalize the supramolecular constructs, assembled from 3’-/5’-end TPE-modified DNA duplexes. Introduction of a terminal functionality into the duplexes governs the supramolecular assembly process and leads to clearly distinct DNA architectures, such as a star-shaped morphology. Chapter 6 provides an approach for the creation of DNA nanostructures, assembled from 3’-/5’-end TPE-modified DNA conjugates hybridized to a longer DNA complement. In the seventh chapter, the self-assembly of phosphodiester-linked TPE trimers in aqueous medium under different conditions is presented. Chapter 8 briefly describes a collaboration project, namely the synthesis of target compounds that are subsequently employed in on-surface polymerization and cryo-force spectroscopy experiments. Finally, overall conclusions are drawn, as well as outlining future perspectives

Supramolecular assembly of pyrene-DNA conjugates: influence of pyrene substitution pattern and implications for artificial LHCs.

The supramolecular self-assembly of pyrene-DNA conjugates into nanostructures is presented. DNA functionalized with different types of pyrene isomers at the 3'-end self-assemble into nano-objects. The shape of the nanostructures is influenced by the type of pyrene isomer appended to the DNA. Multilamellar vesicles are observed with the 1,6- and 1,8-isomers, whereas conjugates of the 2,7-isomer exclusively assemble into spherical nanoparticles. Self-assembled nano-spheres obtained with the 2,7-dialkynyl pyrene isomer were used for the construction of an artificial light-harvesting complex (LHC) in combination with Cy3 as the energy acceptor

Tetraphenylethylene–DNA conjugates: influence of sticky ends and DNA sequence length on the supramolecular assembly of AIE-active vesicles

The supramolecular assembly of DNA conjugates, functionalized with tetraphenylethylene (TPE) sticky ends, into vesicular structures is described. The aggregation-induced emission (AIE) active TPE units allow to monitor the assembly process by fluorescence spectroscopy. The number of TPE modifications in the overhangs of the conjugates influences the supramolecular assembly behavior. A minimum of two TPE residues on each end are required to ensure a well-defined assembly process. The design of the presented DNA-based nanostructures offers tailored functionalization with applications in DNA nanotechnology

Swiss general internal medicine board examination: quantitative effects of publicly available and unavailable questions on question difficulty and test performance.

BACKGROUND Formerly, a substantial number of the 120 multiple-choice questions of the Swiss Society of General Internal Medicine (SSGIM) board examination were derived from publicly available MKSAP questions (Medical Knowledge Self-Assessment Program®). The possibility to memorise publicly available questions may unduly influence the candidates' examination performance. Therefore, the examination board raised concerns that the examination did not meet the objective of evaluating the application of knowledge. The society decided to develop new, "Helvetic" questions to improve the examination. The aim of the present study was to quantitatively assess the degree of difficulty of the Helvetic questions (HQ) compared with publicly available and unavailable MKSAP questions and to investigate whether the degree of difficulty of MKSAP questions changed over time as their status changed from publicly available to unavailable. METHODS The November 2019 examination consisted of 40 Helvetic questions, 40 publicly available questions from MKSAP edition 17 (MKSAP-17) and 40 questions from MKSAP-15/16, which were no longer publicly available at the time of the examination. An one factorial univariate analysis of variance (ANOVA) examined question difficulty (lower values mean higher difficulty) between these three question sets. A repeated ANOVA compared the difficulty of MKSAP-15/16 questions in the November 2019 examination with the difficulty of the exact same questions from former examinations, when these questions belonged to the publicly available MKSAP edition. The publicly available MKSAP-17 and the publicly unavailable Helvetic questions served as control. RESULTS The analysis of the November 2019 exam showed a significant difference in average item difficulty between Helvetic and MKSAP-17 questions (71% vs 86%, p <0.001) and between MKSAP-15/16 and MKSAP-17 questions (70% vs 86%, p <0.001). There was no significant difference in item difficulty between Helvetic and MKSAP-15/16 questions (71% vs 70%, p = 0.993). The repeated measures ANOVA on question use and the three question categories showed a significant interaction (p <0.001, partial eta-squared = 0.422). The change in the availability of MKSAP-15/16 questions had a strong effect on difficulty. Questions became on average 21.9% more difficult when they were no longer publicly available. In contrast, the difficulty of the MKSAP-17 and Helvetic questions did not change significantly across administrations. DISCUSSION This study provides the quantitative evidence that the public availability of questions has a decisive influence on question difficulty and thus on SSGIM board examination performance. Reducing the number of publicly available questions in the examination by introducing confidential, high-quality Helvetic questions contributes to the validity of the board examination by addressing higher order cognitive skills and making rote-learning strategies less effective

Supramolecular assembly of DNA-constructed vesicles

The self-assembly of DNA hybrids possessing tetraphenylethylene sticky ends at both sides into vesicular architectures in aqueous medium is demonstrated. Cryo-electron microscopy reveals the formation of different types of morphologies from the amphiphilic DNA-hybrids. Depending on the conditions, either an extended (sheet-like) or a compact (columnar) alignment of the DNA hybrids is observed. The different modes of DNA arrangement lead to the formation of vesicles appearing either as prolate ellipsoids (type I) or as spheres (type II). The type of packing has a significant effect on the accessibility of the DNA, as evidenced by intercalation and light-harvesting experiments. Only the vesicles exhibiting the sheet-like DNA alignment are accessible for intercalation by ethidium bromide or for the integration of chromophore-labelled DNA via a strand exchange process. The dynamic nature of type I vesicles enables their elaboration into artificial light-harvesting complexes by DNA-guided introduction of Cy3-acceptor chromophores. DNA-constructed vesicles of the kind shown here represent versatile intermediates that are amenable to further modification for tailored nanotechnology applications

Self-assembly of a Bolaamphiphilic Cyclopenta[hi]aceanthrylene Derivative in Aqueous Medium

A low optical bandgap and fullerene-like electron affinity of functionalized cyclopenta[hi]aceanthrylene (cypac) was reported and potential applications as electron acceptors in organic solar cells are suggested among others.[1] In this work, a bolaamphiphilic cypac derivative was synthesized, which exhibits absorbance over the entire visible spectrum and self-assembles in aqueous medium into a vesicular morphology. The average size distribution of the vesicles can be controlled by the concentration of the monomeric building block cypac-bis-phosphate

AIE-Active Supramolecular Assemblies of TPE-DNA Conjugates

Opposite to many chromophores that suffer from aggregation-caused quenching (ACQ), aggregation-induced emission (AIE) type chromophores exhibit intense fluorescence and efficient energy transfer in molecular assemblies. That is why aggregation-induced emitters have gained much attention in the fields of optoelectronic devices and the creation of artificial light-harvesting systems among others.[1] Previous work demonstrated light-harvesting in supramolecular vesicles assembled from phenanthrene-DNA conjugates.[2] In this work, the phenanthrenes have been replaced by either E-tetraphenylethylenes (TPEs) (Figure 1A) or Z-TPEs and resulted in the formation of AIE-active supramolecular assemblies. As evidenced by AFM, duplex 1 self-assembles in aqueous medium into spherical objects (Figure 1B). Similar results are also obtained for Z-TPE-modified DNA conjugates. Spectroscopic data as well as physicochemical properties of the supramolecular arrays will be presented and discussed on this poster

Visusstörungen in der Tumordiagnostik – Aderhautmetastasen

Choroidal metastasis represents the most common type of intraocular malignancy and preferably involves the posterior uveal tract. Breast and lung cancer - known or so far undiagnosed - are most frequently identified as the underlying tumor disease. The majority of patients diagnosed with uveal metastasis have additional metastatic manifestations elsewhere, so re-staging before treatment is recommended. The importance of a multidisciplinary approach is obvious. Early diagnosis and timely initiation of treatment are mandatory in case of vision-threatening situations. External beam radiation remains the therapy of choice. Overall survival of patients with uveal metastasis is limited, averaging six to twelve months. The other eye is frequently enough affected as well, justifying regular ophthalmologic follow-up during the further course of the disease.Eine Metastase eines Karzinoms ist der häufigste intraokuläre Tumor, und sie lokalisiert sich meist im Bereich der posterioren Uvea. Als Primärtumor findet man vorzugsweise ein (bekanntes oder unbekanntes) Mammakarzinom oder ein Bronchialkarzinom. Die überwiegende Mehrheit der Patienten hat bei Diagnose von Aderhautmetastasen weitere Metastasen, so dass ein Re-Staging sinnvoll sein kann. Die Notwendigkeit zur interdisziplinären Betreuung aufgrund der Lokalisation ist offensichtlich. Bei Visusbedrohung sind schnelle Diagnostik und Einleitung der Therapie entscheidend. Eine externe Strahlentherapie ist die Methode der Wahl. Die Überlebenszeit von Patienten mit Aderhautmetastasen ist kurz und beträgt median sechs bis zwölf Monate. Da auch das Partnerauge von Aderhautmetastasen betroffen sein kann, sind aus diesem Grund ophthalmologische Verlaufskontrollen sinnvoll

Complex DNA Architectonics─Self-Assembly of Amphiphilic Oligonucleotides into Ribbons, Vesicles, and Asterosomes.

The precise arrangement of structural subunits is a key factor for the proper shape and function of natural and artificial supramolecular assemblies. In DNA nanotechnology, the geometrically well-defined double-stranded DNA scaffold serves as an element of spatial control for the precise arrangement of functional groups. Here, we describe the supramolecular assembly of chemically modified DNA hybrids into diverse types of architectures. An amphiphilic DNA duplex serves as the sole structural building element of the nanosized supramolecular structures. The morphology of the assemblies is governed by a single subunit of the building block. The chemical nature of this subunit, i.e., polyethylene glycols of different chain length or a carbohydrate moiety, exerts a dramatic influence on the architecture of the assemblies. Cryo-electron microscopy revealed the arrangement of the individual DNA duplexes within the different constructs. Thus, the morphology changes from vesicles to ribbons with increasing length of a linear polyethylene glycol. Astoundingly, attachment of a N-acetylgalactosamine carbohydrate to the DNA duplex moiety produces an unprecedented type of star-shaped architecture. The novel DNA architectures presented herein imply an extension of the current concept of DNA materials and shed new light on the fast-growing field of DNA nanotechnology