Aptamer micro-factories: replacing SELEX by a single-step aptamer selection strategy.

Aptamers are single stranded oligonucleotides that, similarly to antibodies, bind their targets with great affinity and specificity by adopting a defined 2D/3D structure. Aptamers have been widely employed as target recognition molecules in diagnostics and are currently being introduced in the clinic as therapeutics. Isolation of new aptamers is a non-trivial process relying on an in vitro method termed SELEX, based on the iterative collection of the best candidates from a vast pool of random oligonucleotides. This project aims at developing an innovative and rapid single-step aptamer selection strategy by integrating three novel concepts. First, the large random libraries will be replaced by a smaller pool of oligonucleotides designed in silico for their ability to form highly stable structures. Second, the pre-designed library containing only the most relevant sequences will be immobilized on a digital microfluidic chip and amplified through a procedure called rolling circle amplification. Finally, after incubation with the molecule of interest, using innovative optical technologies, aptamers that have bound to the target will be identified, selectively detached and collected from the chip surface. The proposed concept will create a large impact in food and medical diagnostics. To achieve these goals two young and dynamic research groups from KU Leuven with expertise in biosensors and advanced optical microscopy will join forces.