TectoRNA and 'kissing-loop' RNA: atomic force microscopy of self-assembling RNA structures

Area of Science:

• Biophysics
• Molecular Biology
• Nanotechnology

Background:

• Atomic force microscopy (AFM) is less frequently applied to RNA than DNA.
• RNA molecules can self-assemble into complex supramolecular structures.
• Understanding RNA self-assembly is crucial for various biological and nanotechnological applications.

Purpose of the Study:

• To present AFM imaging of two distinct self-assembling RNA systems.
• To characterize the supramolecular architectures formed by these RNA molecules.
• To explore methods and limitations for measuring molecular volumes from AFM data.

Main Methods:

• Atomic Force Microscopy (AFM) for high-resolution imaging of RNA molecules.
• Analysis of RNA self-assembly into dimers and fibers.
• Image processing techniques for molecular volume estimation.

Main Results:

• AFM imaging revealed a 230-nt murine leukaemia virus RNA fragment forming elongated dimers via 'kissing-loop' interactions.
• Supramolecular fibers composed of artificial tectoRNA units were visualized, with lengths suggesting 50-70 units per fiber.
• Methods for determining molecular volumes from AFM images were discussed, alongside their inherent limitations.

Conclusions:

• AFM is a viable technique for visualizing complex RNA supramolecular structures.
• The study provides insights into the self-assembly mechanisms of viral and artificial RNA.
• This work contributes to the understanding of RNA nanostructures and AFM-based molecular measurements.