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

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.