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Exploiting conformational changes in a caffeine aptamer to engineer synthetic RNA devices.

Leon Kraus1, Vincent J Gunawan1, Robin Johannson1

  • 1Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany.

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Researchers developed a new caffeine-binding RNA aptamer using advanced selection methods. This modular aptamer regulates RNA devices in yeast and mammalian cells, expanding synthetic biology tools.

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Area of Science:

  • Synthetic biology
  • Molecular biology
  • RNA nanotechnology

Background:

  • RNA devices like riboswitches are crucial for synthetic biology.
  • Limited availability of conformation-switching aptamers hinders RNA device development, especially in mammalian systems.
  • Traditional selection methods often fail to identify aptamers with desired conformational changes.

Purpose of the Study:

  • To address the scarcity of conformation-switching aptamers.
  • To select a caffeine-binding aptamer for modular integration into RNA devices.
  • To establish robust strategies for aptamer integration in diverse RNA platforms.

Main Methods:

  • RNA Capture-SELEX and in vivo screenings were used to select a caffeine-binding aptamer.
  • Optifluidic screenings were employed to overcome challenges in ribozyme screening for mammalian systems.
  • A grafting method was used to create a fluorogenic aptasensor.

Main Results:

  • A novel caffeine-binding aptamer was successfully selected.
  • The aptamer demonstrated modular regulation of riboswitches and ribozymes in yeast and mammalian cells.
  • The aptamer was transformed into a functional fluorogenic aptasensor.

Conclusions:

  • The selected aptamer is modular and communicates effectively with RNA devices.
  • Robust strategies for modular aptamer integration were established.
  • This work broadens the aptamer repertoire and advances RNA-based synthetic biology.