Synthesis and characterisation of photoreactive silanes for the self-assembly on functionalised silica surfaces

The aim of this thesis was to investigate novel techniques to create complex hierarchical chemical patterns on silica surfaces with micro to nanometer sized features. These surfaces were used for a site-selective assembly of colloidal particles and oligonucleotides. To do so, functionalised alkoxysilanes (commercial and synthesised ones) were deposited onto planar silica surfaces. The functional groups can form reversible attractive interactions with the complementary surface layers of the opposing objects that need to be assembled. These interactions determine the final location and density of the objects onto the surface. Photolithographically patterned silica surfaces were modified with commercial silanes, in order to create hydrophilic and hydrophobic regions on the surface. Assembly of hydrophobic silica particles onto these surfaces was investigated and finally, pH and charge effects on the colloidal assembly were analysed. In the second part of this thesis the concept of novel, "smart" alkoxysilanes is introduced that allows parallel surface activation and patterning in a one-step irradiation process. These novel species bear a photoreactive head-group in a protected form. Surface layers made from these molecules can be irradiated through a mask to remove the protecting group from selected regions and thus generate lateral chemical patterns of active and inert regions on the substrate. The synthesis of an azide-reactive alkoxysilane was successfully accomplished. Silanisation conditions were carefully optimised as to guarantee a smooth surface layer, without formation of micellar clusters. NMR and DLS experiments corroborated the absence of clusters when using neither water nor NaOH as catalysts during hydrolysis, but only the organic solvent itself. Upon irradiation of the azide layer, the resulting nitrene may undergo a variety of reactions depending on the irradiation conditions. Contact angle measurements demonstrated that the irradiated surfaces were more hydrophilic than the non-irradiated azide layer and therefore the formation of an amine upon irradiation was postulated. Successful photoactivation could be demonstrated using condensation patterns, which showed a change in wettability on the wafer surface upon irradiation. Colloidal deposition with COOH functionalised particles further underlined the formation of more hydrophilic species. Orthogonal photoreactive silanes are described in the third part of this thesis. The advantage of orthogonal photosensitive silanes is the possibility of having a coexistence of chemical functionalities homogeneously distributed in the same layer, by using appropriate protecting groups. For this purpose, a 3',5'-dimethoxybenzoin protected carboxylic acid silane was successfully synthesised and the kinetics of its hydrolysis and condensation in solution were analysed in order to optimise the silanisation conditions. This compound was used together with a nitroveratryl protected amino silane to obtain bicomponent surface layers. The optimum conditions for an orthogonal deprotection of surfaces modified with this two groups were determined. A 2-step deprotection process through a mask generated a complex pattern on the substrate by activating two different chemistries at different sites. This was demonstrated by colloidal adsorption and fluorescence labelling of the resulting substrates. Moreover, two different single stranded oligodeoxynucleotides were immobilised onto the two different activated areas and then hybrid captured with their respective complementary, fluorescent labelled strand. Selective hybridisation could be shown, although non-selective adsorption issues need to be resolved, making this technique attractive for possible DNA microarrays.

DNA block copolymers - synthesis, morphologies and applications

The last decades have witnessed significant and rapid progress in polymer chemistry and molecular biology. The invention of PCR and advances in automated solid phase synthesis of DNA have made this biological entity broadly available to all researchers across biological and chemical sciences. Thanks to the development of a variety of polymerization techniques, macromolecules can be synthesized with predetermined molecular weights and excellent structural control. In recent years these two exciting areas of research converged to generate a new type of nucleic acid hybrid material, consisting of oligodeoxynucleotides and organic polymers. By conjugating these two classes of materials, DNA block copolymers are generated exhibiting engineered material properties that cannot be realized with polymers or nucleic acids alone. Different synthetic strategies based on grafting onto routes in solution or on solid support were developed which afforded DNA block copolymers with hydrophilic, hydrophobic and thermoresponsive organic polymers in good yields. Beside the preparation of DNA block copolymers with a relative short DNA-segment, it was also demonstrated how these bioorganic polymers can be synthesized exhibiting large DNA blocks (>1000 bases) applying the polymerase chain reaction. Amphiphilic DNA block copolymers, which were synthesized fully automated in a DNA synthesizer, self-assemble into well-defined nanoparticles. Hybridization of spherical micelles with long DNA templates that encode several times the sequence of the micelle corona induced a transformation into rod-like micelles. The Watson-Crick motif aligned the hydrophobic polymer segments along the DNA double helix, which resulted in selective dimer formation. Even the length of the resulting nanostructures could be precisely adjusted by the number of nucleotides of the templates. In addition to changing the structural properties of DNA-b-PPO micelles, these materials were applied as 3D nanoscopic scaffolds for organic reactions. The DNA strands of the corona were organized by hydrophobic interactions of the organic polymer segments in such a fashion that several DNA-templated organic reactions proceeded in a sequence specific manner; either at the surface of the micelles or at the interface between the biological and the organic polymer blocks. The yields of reactions employing the micellar template were equivalent or better than existing template architectures. Aside from its physical properties and the morphologies achieved, an important requirement for a new biomaterial is its biocompatibility and interaction with living systems, i.e. human cells. The toxicity of the nanoparticles was analyzed by a cell proliferation assay. Motivated by the non-toxic nature of the amphiphilic DNA block copolymers, these nanoobjects were employed as drug delivery vehicles to target the anticancer drug to a tumor tissue. The micelles obtained from DNA block copolymers were easily functionalized with targeting units by hybridization. This facile route allowed studying the effect of the amount of targeting units on the targeting efficacy. By varying the site of functionalization, i.e. 5’ or 3’, the outcome of having the targeting unit at the periphery of the micelle or in the core of the micelle was studied. Additionally, these micelles were loaded with an anticancer drug, doxorubicin, and then applied to tumor cells. The viability of the cells was calculated in the presence and absence of targeting unit. It was demonstrated that the tumor cells bearing folate receptors showed a high mortality when the targeting unit was attached to the nanocarrier.