First contact imaging of nanoparticular siRNA – From synthesis to application of a prodye concept

Delivery of therapeutic nucleic acid based drugs is still very demanding and difficult to manage and monitor. For this reason, a precise method for the monitoring of RNAi pathways is necessary. This thesis explores a new approach for sensing of potentially therapeutic nucleic acids, using the interaction of so called prodyes with intracellular enzymes in a prodrug manner. To realize this concept, some non-fluorescent, fluorescein based asymmetric dyes were synthesized and their spectroscopic characteristics were studied. Azide-alkyne Click chemistry was applied for conjugation purposes, using a new protocol at weak acidic pH to get intact prodye constructs. Both, an electrophoretic mobility shift assay with polyacrylamide gels and in-cuvette experiments showed remarkable OFF-to-ON behavior of these new siRNA constructs under physiological conditions. After salt-free purification, subsequent hybridization to double-stranded ribonucleic acids and nanoformulation to lipoplexes, the prodye conjugated siRNA was examined in cellular uptake studies for First Contact Imaging. The investigated siRNA-prodye conjugates showed strong sensitivity to esterases, being hydrolyzed at the biolabile function and developing a strong fluorescence which was verified in bulk. As an optimization, a new profluorescent molecule system was designed and synthesized, which has a carbonate as biolabile 6’ protecting group and a highly water soluble 3’ clickable linker. This new non-fluorescent but colored prodye showed 12 - 320 times increased fluorescence intensities between OFF- and ON- states, depending to the deprotection method. This is the first reported molecule model of an asymmetric profluorescent fluorescein, having the very favorable 3’ & 6’ functions.

Metodología para la asignación de vehículos de una flota a rutas preestablecidas

En general, la distribución de una flota de vehículos que recorre rutas fijas no se realiza completamente en base a criterios objetivos, primando otros aspectos más difícilmente cuantificables. El análisis apropiado debería tener en consideración la variabilidad existente entre las diferentes rutas dentro de una misma ciudad para así determinar qué tecnología es la que mejor se adapta a las características de cada itinerario. Este trabajo presenta una metodología para optimizar la asignación de una flota de vehículos a sus rutas, consiguiendo reducir el consumo y las emisiones contaminantes. El método propuesto está organizado según el siguiente procedimiento: - Registro de las características cinemáticas de los vehículos que recorren un conjunto representativo de rutas. - Agrupamiento de las líneas en conglomerados de líneas similares empleando un algoritmo jerárquico que optimice el índice de semejanza entre rutas obtenido mediante contraste de hipótesis de las variables representativas. - Generación de un ciclo cinemático específico para cada conglomerado. - Tipificación de variables macroscópicas que faciliten la clasificación de las restantes líneas utilizando una red neuronal entrenada con la información recopilada en las rutas medidas. - Conocimiento de las características de la flota disponible. - Disponibilidad de un modelo que estime, según la tecnología del vehículo, el consumo y las emisiones asociados a las variables cinemáticas de los ciclos. - Desarrollo de un algoritmo de reasignación de vehículos que optimice una función objetivo dependiente de las emisiones. En el proceso de optimización de la flota se plantean dos escenarios de gran trascendencia en la evaluación ambiental, consistentes en minimizar la emisión de dióxido de carbono y su impacto como gas de efecto invernadero (GEI), y alternativamente, la producción de nitróxidos, por su influencia en la lluvia ácida y en la formación de ozono troposférico en núcleos urbanos. Además, en ambos supuestos se introducen en el problema restricciones adicionales para evitar que las emisiones de las restantes sustancias superen los valores estipulados según la organización de la flota actualmente realizada por el operador. La metodología ha sido aplicada en 160 líneas de autobús de la EMT de Madrid, conociéndose los datos cinemáticos de 25 rutas. Los resultados indican que, en ambos supuestos, es factible obtener una redistribución de la flota que consiga reducir significativamente la mayoría de las sustancias contaminantes, evitando que, en contraprestación, aumente la emisión de cualquier otro contaminante. ABSTRACT In general, the distribution of a fleet of vehicles that travel fixed routes is not usually implemented on the basis of objective criteria, thus prioritizing on other features that are more difficult to quantify. The appropriate analysis should consider the existing variability amongst the different routes within the city in order to determine which technology adapts better to the peculiarities of each itinerary. This study proposes a methodology to optimize the allocation of a fleet of vehicles to the routes in order to reduce fuel consumption and pollutant emissions. The suggested method is structured in accordance with the following procedure: - Recording of the kinematic characteristics of the vehicles that travel a representative set of routes. - Grouping of the lines in clusters of similar routes by utilizing a hierarchical algorithm that optimizes the similarity index between routes, which has been previously obtained by means of hypothesis contrast based on a set of representative variables. - Construction of a specific kinematic cycle to represent each cluster of routes. - Designation of macroscopic variables that allow the classification of the remaining lines using a neural network trained with the information gathered from a sample of routes. - Identification and comprehension of the operational characteristics of the existing fleet. - Availability of a model that evaluates, in accordance with the technology of the vehicle, the fuel consumption and the emissions related with the kinematic variables of the cycles. - Development of an algorithm for the relocation of the vehicle fleet by optimizing an objective function which relies on the values of the pollutant emissions. Two scenarios having great relevance in environmental evaluation are assessed during the optimization process of the fleet, these consisting in minimizing carbon dioxide emissions due to its impact as greenhouse gas (GHG), and alternatively, the production of nitroxides for their influence on acid rain and in the formation of tropospheric ozone in urban areas. Furthermore, additional restrictions are introduced in both assumptions in order to prevent that emission levels for the remaining substances exceed the stipulated values for the actual fleet organization implemented by the system operator. The methodology has been applied in 160 bus lines of the EMT of Madrid, for which kinematic information is known for a sample consisting of 25 routes. The results show that, in both circumstances, it is feasible to obtain a redistribution of the fleet that significantly reduces the emissions for the majority of the pollutant substances, while preventing an alternative increase in the emission level of any other contaminant.

Structure and function in rhodopsin: Topology of the C-terminal polypeptide chain in relation to the cytoplasmic loops*

Cysteine mutagenesis and site-directed spin labeling in the C-terminal region of rhodopsin have been used to probe the local structure and proximity of that region to the cytoplasmic loops. Each of the native amino acids in the sequence T335–T340 was replaced with Cys, one at a time. The sulfhydryl groups of all mutants reacted rapidly with the sulfhydryl reagent 4,4′-dithiodipyridine, which indicated a high degree of solvent accessibility. Furthermore, to probe the proximity relationships, a series of double Cys mutants was constructed. One Cys in all sets was at position 338 and the other was at a position in the sequence S240–V250 in the EF interhelical loop, at position 65 in the AB interhelical loop, or at position 140 in the CD interhelical loop. In the dark state, no significant disulfide formation was observed between C338 and C65 or C140 under the conditions used, whereas a relatively rapid disulfide formation was observed between C338 and C242 or C245. Spin labels in the double Cys mutants showed the strongest magnetic interactions between the nitroxides attached to C338 and C245 or C246. Light activation of the double mutant T242C/S338C resulted in slower disulfide formation, whereas interactions between nitroxides at C338 and C245 or C246 decreased. These results suggest the proximity of the C-terminal residue C338 to residues located on the outer face of a cytoplasmic helical extension of the F helix with an apparent increase of distance upon photoactivation.

Site-directed spin labeling and chemical crosslinking demonstrate that helix V is close to helices VII and VIII in the lactose permease of Escherichia coli.

Site-directed chemical cleavage of lactose permease indicates that helix V is in close proximity to helices VII and VIII. To test this conclusion further, permease containing a biotin-acceptor domain and paired Cys residues at positions 148 (helix V) and 228 (helix VII), 148 and 226 (helix VII), or 148 and 275 (helix VIII) was affinity purified and labeled with a sulfhydryl-specific nitroxide spin label. Spin-spin interactions are observed with the 148/228 and 148/275 pairs, indicating close proximity between appropriate faces of helix V and helices VII and VIII. Little or no interaction is evident with the 148/226 pair, in all likelihood because position 226 is on the opposite face of helix VII from position 228. Broadening of the electron paramagnetic resonance spectra in the frozen state was used to estimate distance between the 148/228 and the 148/275 pairs. The nitroxides at positions 148 and 228 or 148 and 275 are within approximately 13-15 A. Finally, Cys residues at positions 148 and 228 are crosslinked by dibromobimane, a bifunctional crosslinker that is approximately 5 A. long, while no crosslinking is detected between Cys residues at positions 148 and 275 or 148 and 226. The results provide strong support for a structure in which helix V is in close proximity to both helices VII and VIII and is oriented in such a fashion that Cys-148 is closer to helix VII.

Determination of the distance between two spin labels attached to a macromolecule.

An EPR "spectroscopic ruler" was developed using a series of alpha-helical polypeptides, each modified with two nitroxide spin labels. The EPR line broadening due to electron-electron dipolar interactions in the frozen state was determined using the Fourier deconvolution method. These dipolar spectra were then used to estimate the distances between the two nitroxides separated by 8-25 A. Results agreed well with a simple alpha-helical model. The standard deviation from the model system was 0.9 A in the range of 8-25 A. This technique is applicable to complex systems such as membrane receptors and channels, which are difficult to access with high-resolution NMR or x-ray crystallography, and is expected to be particularly useful for systems for which optical methods are hampered by the presence of light-interfering membranes or chromophores.

Applications of EPR with an Emphasis on Tau Fibril Structure

Substances containing unpaired electrons have been studied by electron paramagnetic resonance (EPR) for nearly 70 years. With continual development and enhancement of EPR techniques, questions have arisen regarding optimum method selection for a given sample based on its properties. In this work, radiation defects, natural lattice defects, solid organic radicals, radicals in solution, and spin-labeled proteins were analyzed using CW, pulse, and rapid scan EPR to compare methods. Studies of solid BDPA, EOe in quartz, Ns0 in diamond, and a-Si:H, showed that rapid scan could overcome many obstacles presented by other techniques, cementing rapid scan as an effective alternative to CW and pulse methods. Relaxation times of six nitroxide radicals were characterized from 0.25-34 GHz, guiding synthesis of improved nitroxides for in vivo imaging experiments. Processes contributing to T1 of DPPH in polystyrene were found through variable temperature measurements at X- and Q-band, resolving previously-reported discrepancies in relaxation properties and providing new insight into this commonly-used standard. In the history of EPR, the study of proteins is relatively new. Double electron-electron resonance (DEER) has emerged as a powerful technique for the study of amyloid fibrils, a class of protein aggregates implicated in a number of neurodegenerative disorders. Microtubule-associated protein tau forms fibrils linked to Alzheimerfs disease through seeded conversion of monomer. Self-assembly is mediated by the microtubule binding repeats in tau, and there are either three or four repeats present depending on the isoform. DEER was used to show that filaments of 3R and 4R tau are conformationally distinct and that 4R fibrils adopt a heterogeneous mixture of conformations. Populations of 4R fibril conformations, which were independently validated using a model system, can be modulated by introduction of mutations to the primary sequence or by varying fibril growth conditions. These findings provided unprecedented insights into the seed selection of tau monomers and established conformational compatibility as an important driving force in tau fibril propagation. Lastly, DEER acquisition was improved through addition of paramagnetic metal to spin-labeled protein, decreasing collection time, and through use of a novel spin label with increased T2, thereby lengthening the available acquisition window.

Rapid Scan Electron Paramagnetic Resonance (EPR) and Digital EPR Development

Rapid scan electron paramagnetic resonance (EPR) was developed in the Eaton laboratory at the University of Denver. Applications of rapid scan to wider spectra, such as for immobilized nitroxides, spin-labeled proteins, irradiated tooth and fingernail samples were demonstrated in this dissertation. The scan width has been increased from 55 G to 160 G. The signal to noise (S/N) improvement for slowly tumbling spin-labeled protein samples that is provided by rapid scan EPR will be highly advantageous for biophysical studies. With substantial improvement in S/N by rapid scan, the dose estimation for irradiated tooth enamels became more reliable than the traditional continuous wave (CW) EPR. An alternate approach of rapid scan, called field-stepped direct detection EPR, was developed to reconstruct wider EPR signals. A Mn2+ containing crystal was measured by field-stepped direct detection EPR, which had a spectrum more than 6000 G wide. Since the field-stepped direct detection extends the advantages of rapid scan to much wider scan ranges, this methodology has a great potential to replace the traditional CW EPR. With recent advances in digital electronics, a digital rapid scan spectrometer was built based on an arbitrary waveform generator (AWG), which can excite spins and detect EPR signals with a fully digital system. A near-baseband detection method was used to acquire the in-phase and quadrature signals in one physical channel. The signal was analyzed digitally to generate ideally orthogonal quadrature signals. A multiharmonic algorithm was developed that employed harmonics of the modulation frequencies acquired in the spectrometer transient mode. It was applied for signals with complicated lineshapes, and can simplify the selection of modulation amplitude. A digital saturation recovery system based on an AWG was built at X-band (9.6 GHz). To demonstrate performance of the system, the spin-lattice relaxation time of a fused quartz rod was measured at room temperature with fully digital excitation and detection.

An investigation of the nitroxide-mediated preirradiation grafting of styrene onto PFA

Simultaneous and preirradiation grafting of styrene onto fluorinated polyolefins does not enable control of the molecular weights or polydispersities of the styrene grafts. The nitroxide-mediated grafting of styrene onto PFA with TEMPO and TEISO using a preirradiation method has been investigated as a means of controlling the graft properties and especially to produce grafts with improved suitability for SPOC. The yields of graft were found to be in the range 15-20% for nitroxide concentrations between 5 x 10(-3) and 2 x 10(-2) M and were similar for the two nitroxides studied. Raman mapping was used to obtain the depth profile for the styrene grafts. The grafts were found to be principally located within the PFA substrate, and little graft was formed at the PFA surface. Fmoc loading tests were performed to assess the suitability of the grafted PFA as a support for SPOC, but these showed no significant loading was achieved, thus indicating that the graft properties are not suitable for SPOC. However, the study has important implications for the applications of PFA-grafted polymers in other areas, such as chemically resistant ion-exchange and separation membranes.

The synthesis of a ferromagnetic polymer

The aim of this study was to prepare a ferromagnetic polymer using the design elements of molecular magnets. This involved the preparation of co-polyradicals of phenylacetylenes bearing nitronyl nitroxides and nitro/cyano groups. The magnetic properties of the materials were determined using a SQUID magnetometer. A novel rhodium catalyst, Rh(NBD)(NH3)Cl, was prepared in order to obtain good yields of polymerisation. A wide range of substituted phenylacetylenes were first homopolymerised in order to assess the efficiency of the catalyst. Yields were generally high, between 75% and 98%, and the time of polymerisation was short (one hour). SEC analysis revealed that the Mw of the polymers were in the range of 200,000 and 250,000. The discovery that phenylboronic acid acts a co-catalyst for the polymerisation served to increase the yields by 10% to 20% but the Mw of the polymers was reduced to approximately 100,000. Co-polyradicals were prepared in good to excellent yield using the new catalyst. The magnetic properties in the temperature range of 300K to 1.8K were investigated by SQUID, which revealed a spin glass system, antiferromagnets and possible dipolar magnets. Short-range ferromagnetic interactions between 300K and 100K were found in a co-polyradical containing nitronyl nitroxide and cyano substituted monomers. The magnetic properties were dependent upon both the type of monomers utilised and the ratio between them. The effects of ring substituents on the terminal alkyne have been studied by carbon-13 NMR. There was no correlation however, between the chemical shift of terminal alkyne and the polymerisability of the monomer.