Programmable Edge-to-Edge Assembly of RNA Nanostructures

Area of Science:

• RNA nanotechnology
• Molecular self-assembly
• Biomolecular engineering

Background:

• Complex RNA nanostructures require precise molecular connectors for controlled self-assembly.
• Existing connectors, like kissing loops, are limited to coaxial joining, restricting achievable geometries.

Purpose of the Study:

• To introduce a novel RNA connector, the alpha kissing loop (alphaKL), for versatile helix association.
• To enable edge-to-edge helix connections, expanding the design space for RNA nanostructures.

Main Methods:

• Development of the alpha kissing loop (alphaKL) combining kissing loop and triplex interactions.
• Incorporation of alphaKLs into RNA origami tiles for multivalent assembly.
• Characterization using atomic force microscopy and molecular dynamics simulations.

Main Results:

• AlphaKLs successfully drove the assembly of RNA origami tiles into filaments and lattices.
• Molecular dynamics revealed sequence-dependent control over interhelical angles via triplex occupancy.
• Cooperative backbone contacts enhanced the rigidity of multi-alphaKL interfaces.

Conclusions:

• The alpha kissing loop (alphaKL) provides a novel, sequence-programmable method for edge-to-edge RNA helix association.
• This expands the accessible geometric designs for RNA nanostructures, overcoming limitations of previous connectors.
• AlphaKLs facilitate the construction of complex, previously unattainable RNA architectures.