The ability to modify the properties of materials by controlling their structure at nanoscale makes them extremely attractive for many applications: from fundamental scientific studies to commercially realizable technologies. In the biological context a variety of nanomaterials promise to offer sensitive, rapid and cost-effective solutions for modern clinical laboratory. In particular, dye-doped silica nanoparticles (NPs) have been demonstrated to be sensitive labeling markers for biosensing and bioimaging. Their flexible conjugation, excellent photostability, and ultrasensitivity make them a powerful tool in bioanalysis. Indeed luminescent dye-doped nanoparticles are excellent candidates for biological applications because (1) they can be analyzed with the standard existing tools (microarray scanners, optical fluorescence microscopes), which are fitted for standard fluorophore excitation and emission curves, (2) a large number of dye molecules can be incorporated in a single particle, increasing the optical signal and (3) the silica matrix provides a protective barrier minimizing photobleaching and photodegradation. A very efficient synthesis strategy for silica nanoparticles is the Stöber method, which has the advantage that it can be easily scaled up for commercial production and the possibility to effortlessly transfer the nanoparticles into aqueous solutions (typically required for bioanalysis applications). However, modifications on the synthesis process are required to obtain luminescent particles and proper investigation on the particles size control and on the dye-doping process are needed. In this chapter we describe a modifyedStöber synthesis which is based on the use of 3-Aminopropyl-triethoxysilane (APTES) for the efficient incorporation of dye molecules into the silica NPs. The parameters of the modified synthesis have been systematically investigated in order to optimize their morpho-optical properties and to maximize their optical efficiency. Moreover the application of these luminescent silica nanoparticles to DNA microarray technology is also reported for a specific case study: the detection of carcinogenic risky Human Papilloma Virus, which is one of the primary causes for cervical cancer in women worldwide. In particular, DNA microarray is a powerful tool for the parallel, high-throughput detection and quantification of many nucleic acids and other biologically significant molecules. We show that our luminescent silica nanoparticles in comparison to conventional dye labelling or commercial quantum dots allow achieving a significant tenfold increase in the optical signal, and a related decrease of the limit of detection, thus giving a remarkable improvement in this technique towards early diagnosis of the disease. It is worth noticing the fact that this result can be easily transferred to other pathologies and to other fields like for example trace level detection of dangerous biological contaminants in food or in the environment.
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