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

Developments in medical diagnostics, environmental monitoring, food safety and therapeutics require systems that make it possible to detect a wide range of molecules in a fast and easy, yet specific and sensitive manner. In light of these applications and driven by this demand, the field of biosensing has demonstrated huge potential. In spite of this potential, continuous improvements beyond the state of the art are necessary to help overcome remaining challenges and create new opportunities. Among others, the challenges can be correlated with three pivotal aspects of a biosensor: (i) the performance of the bioreceptor molecules, (ii) the nanoarchitecture of the biorecognition layer and (iii) the adequate signal generation.

Although protein elements are frequently adopted as bioreceptors or signal amplifiers in biosensing applications, they often suffer from certain drawbacks related to their limited design flexibility and stability, the latter both in time and in varying assay conditions. Moreover, although highly relevant, the nanoarchitecture of the biorecognition layer (i.e. the bioreceptor positioning at the biosensing interface) is often neglected. In this context, the field of DNA-nanotechnology offers a number of solutions: (1) functional DNA nanotechnology forms an alternative for protein bioreceptors, (2) structural DNA nanotechnology can be applied to control the nanoarchitecture of the biorecognition layer and (3) dynamic DNA nanotechnology is known to enable extensive signal amplification. In this context, the goal of this dissertation was to exploit DNA nanotechnology (DNA probes and aptamers, DNA origami, DNA cascades) as a toolbox to design and develop novel DNA-based strategies for improved biosensing, with the final aim of moving towards DNA-only biosensors.