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A light-responsive RNA aptamer for an azobenzene derivative

DOI:10.1093/nar/gky1225 期刊:Nucleic Acids Research 出版年份:2018 更新时间:2025-09-09 09:28:46
摘要: Regulation of complex biological networks has proven to be a key bottleneck in synthetic biology. Interactions between the structurally flexible RNA and various other molecules in the form of riboswitches have shown a high-regulation specificity and efficiency and synthetic riboswitches have filled the toolbox of devices in many synthetic biology applications. Here we report the development of a novel, small molecule binding RNA aptamer, whose binding is dependent on light-induced change of conformation of its small molecule ligand. As ligand we chose an azobenzene because of its reliable photoswitchability and modified it with chloramphenicol for a better interaction with RNA. The synthesis of the ligand ‘azoCm’ was followed by extensive biophysical analysis regarding its stability and photoswitchability. RNA aptamers were identified after several cycles of in vitro selection and then studied regarding their binding specificity and affinity toward the ligand. We show the successful development of an RNA aptamer that selectively binds to only the trans photoisomer of azoCm with a KD of 545 nM. As the aptamer cannot bind to the irradiated ligand (λ = 365 nm), a light-selective RNA binding system is provided. Further studies may now result in the engineering of a reliable, light-responsible riboswitch.
作者: Thea S. Lotz,Thomas Halbritter,Christoph Kaiser,Martin M. Rudolph,Leon Kraus,Florian Groher,Sabrina Steinwand,Josef Wachtveitl,Beatrix Suess,Alexander Heckel
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To create a light-dependent synthetic riboswitch with structural changes only occurring upon binding to one photoisomer of a ligand.

The study successfully developed an RNA aptamer that selectively binds to the trans photoisomer of azoCm with high affinity (KD of 545 nM) and shows no binding to the cis-photoisomer. This system provides a foundation for the engineering of light-responsive synthetic riboswitches, offering a tool for the regulation of gene expression with spatial and temporal precision.

The study focused on the development of a light-responsive RNA aptamer and its initial characterization. Further engineering is required to develop a fully functional light-responsive riboswitch. The applicability in vivo and the efficiency of the system in cellular environments remain to be explored.

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