Gene therapy tools: oligonucleotides and peptides

Genetic mutations can cause a wide range of diseases, e.g. cancer. Gene therapy has the potential to alleviate or even cure these diseases. One of the many gene therapies developed so far is RNA-cleaving deoxyribozymes, short DNA oligonucleotides that specifically bind to and cleave RNA. Since the development of these synthetic catalytic oligonucleotides, the main way of determining their cleavage kinetics has been through the use of a laborious and error prone gel assay to quantify substrate and product at different time-points. We have developed two new methods for this purpose. The first one includes a fluorescent intercalating dye, PicoGreen, which has an increased fluorescence upon binding double-stranded oligonucleotides; during the course of the reaction the fluorescence intensity will decrease as the RNA is cleaved and dissociates from the deoxyribozyme. A second method was developed based on the common denominator of all nucleases, each cleavage event exposes a single phosphate of the oligonucleotide phosphate backbone; the exposed phosphate can simultaneously be released by a phosphatase and directly quantified by a fluorescent phosphate sensor. This method allows for multiple turnover kinetics of diverse types of nucleases, including deoxyribozymes and protein nucleases. The main challenge of gene therapy is often the delivery into the cell. To bypass cellular defenses researchers have used a vast number of methods; one of these are cell-penetrating peptides which can be either covalently coupled to or non-covalently complexed with a cargo to deliver it into a cell. To further evolve cell-penetrating peptides and understand how they work we developed an assay to be able to quickly screen different conditions in a high-throughput manner. A luciferase up- and downregulation experiment was used together with a reduction of the experimental time by 1 day, upscaling from 24- to 96-well plates and the cost was reduced by 95% compared to commercially available assays. In the last paper we evaluated if cell-penetrating peptides could be used to improve the uptake of an LNA oligonucleotide mimic of GRN163L, a telomerase-inhibiting oligonucleotide. The combination of cell-penetrating peptides and our mimic oligonucleotide lead to an IC50 more than 20 times lower than that of GRN163L.

Catalytic Processes Mediated by Metal−Organic Frameworks : Reactivity and Mechanistic Studies

The present thesis describes the development of heterogeneous catalytic methodologies using metal−organic frameworks (MOFs) as porous matrices for supporting transition metal catalysts. A wide spectrum of chemical reactions is covered. Following the introductory section (Chapter 1), the results are divided between one descriptive part (Chapter 2) and four experimental parts (Chapters 3–6). Chapter 2 provides a detailed account of MOFs and their role in heterogeneous catalysis. Specific synthesis methods and characterization techniques that may be unfamiliar to organic chemists are illustrated based on examples from this work. Pd-catalyzed heterogeneous C−C coupling and C−H functionalization reactions are studied in Chapter 3, with focus on their practical utility. A vast functional group tolerance is reported, allowing access to substrates of relevance for the pharmaceutical industry. Issues concerning the recyclability of MOF-supported catalysts, leaching and operation under continuous flow are discussed in detail. The following chapter explores puzzling questions regarding the nature of the catalytically active species and the pathways of deactivation for Pd@MOF catalysts. These questions are addressed through detailed mechanistic investigations which include in situ XRD and XAS data acquisition. For this purpose a custom reaction cell is also described in Chapter 4. The scope of Pd@MOF-catalyzed reactions is expanded in Chapter 5. A strategy for boosting the thermal and chemical robustness of MOF crystals is presented. Pd@MOF catalysts are coated with a protecting SiO2 layer, which improves their mechanical properties without impeding diffusion. The resulting nanocomposite is better suited to withstand the harsh conditions of aerobic oxidation reactions. In this chapter, the influence of the nanoparticles’ geometry over the catalyst’s selectivity is also investigated. While Chapters 3–5 dealt with Pd-catalyzed processes, Chapter 6 introduces hybrid materials based on first-row transition metals. Their reactivity is explored towards light-driven water splitting. The heterogenization process leads to stabilized active sites, facilitating the spectroscopic probing of intermediates in the catalytic cycle.