The ability to detect pathogenic cells is essential for many applications in clinical diagnostics. Great attention has been focused on the field during the last decade, stressing the importance of an early and unequivocal detection of certain diseases for a successful diagnosis and thus, a favourable treatment and prognosis. To achieve this, molecular tools are required that unambiguously recognise appropriate cell surface molecules that come along with disease onset and progression. Aptamers are short single-chained oligo(deoxy)nucleotides that interact with cognate target molecules with high affinity and specificity. Within the last years they gained much attention to be employed as cell–recognition tools. In this research proposal, DNA aptamers that reveal broad-spectrum interaction patterns with cancer cells derived from solid tumours will be employed for developing a robust, multiplex assay format likely to determine molecular fingerprints of the most prevalent and lethal cancers worldwide. Furthermore, the multiplex aptamer-based assay will allow gaining information of the relative expression levels of yet unknown marker proteins present on different cancer cells. This will enable profiling of cancer cells, which is highly convenient for diagnostic monitoring. A second goal is the identification of the molecular targets of the employed aptamers. This will be achieved by using siRNA libraries, essentially covering the entire human genome and the knockdown of putative target molecules. Loss of aptamer binding in relation to employed siRNA molecules will lead to information on cognate aptamer target molecules, and they will be studied as possible new biomarkers candidates.
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