Physicochemically tunable polyfunctionalized RNA square architecture with fluorogenic and ribozymatic properties.

Area of Science:

• RNA nanotechnology
• Biomolecular engineering
• Nanomaterials science

Background:

• RNA nanotechnology enables rational design of nanoarchitectures.
• Current methods rely on fixed angles from natural motifs, limiting size variability.
• Producing RNA architectures with diverse sizes from a single sequence is challenging.

Purpose of the Study:

• To develop an approach for constructing RNA nanoparticles with tunable size and stability.
• To engineer RNA squares with controllable physicochemical properties and functionalities.
• To demonstrate the versatility of this modular design for diverse applications.

Main Methods:

• Tuning the three-way junction (3WJ) motif angle from bacteriophage phi29 pRNA to create 90° RNA squares.
• Modulating the "core" strand and adjusting side lengths for size and property control.
• Incorporating functional motifs (siRNA, ribozyme, fluorogenic RNA) onto the RNA square arms.

Main Results:

• Successfully constructed RNA squares of 5, 10, and 20 nm with tunable size and stability.
• Demonstrated diverse thermodynamic and chemical stabilities for different square sizes.
• Utilized intramolecular 3WJ contacts, avoiding weaker intermolecular interactions.

Conclusions:

• A modular design technique using the 3WJ motif allows for the construction of variable-size RNA squares.
• This approach offers controllable properties and functionalities for diverse applications in engineering, pharmaceuticals, and medicine.
• The method provides a new strategy for fine-tuning physicochemical properties in RNA nanotechnology.