Novel Classes of Photoresponsive DNA Aptamers
Biochemistry
Organic Molecular Chemistry - Synthesis and Characterisation
Final Report Abstract
The goals of the project were (a) the synthesis and (photo)chemical characterization of molecules that are photoswitchable, preferentially in the visible wavelength range, (b) the isolation and characterization of DNA aptamers that can selectively bind individual photoisomers of sufficiently thermostable representatives from (a) with good affinities, and (c) the use of the aptamers obtained in (b) for selected applications in DNA nanotechnology. We have prepared a series of promising and novel photoswitches based on azobenzene derivatives, whose photoisomers are characterized by high thermal stability, to make them suitable for aptamer selections. In the course of the project, two publications from other research groups appeared reporting very similar azobenzene compounds as those targeted in our project, whereupon we modified our research program by discarding one of the originally planned classes of compounds and (re)synthesizing the latter photoswitches instead. We also produced water-soluble variants of these compounds for later use in a capture SELEX procedure. A complete SELEX over 14 cycles of selection was performed on the solid-phase-immobilized target molecule 4-FAB-OH, which we had synthesized and photochemically characterized as one of the first candidate molecules. Unfortunately, subsequent analysis of the enriched DNA library, including qPCR and NGS, did not provide sufficient evidence for the success of this selection. Shortly after the start of the project, the SARS-CoV-2 pandemic broke out, causing massive overall delays in the subsequent course of the project. Accordingly, the research program could not be carried out and completed as originally planned.
