PX DNA triangle oligomerized using a novel three-domain motif

Area of Science:

• Structural DNA nanotechnology
• Supramolecular chemistry
• Nanomaterials engineering

Background:

• Structural DNA nanotechnology commonly utilizes Watson-Crick base pairing for self-assembly.
• Alternative DNA cohesion methods, such as paranemic edge-sharing interactions (PX), offer different assembly possibilities.

Purpose of the Study:

• To explore the formation and application of DNA structures based on PX interactions.
• To demonstrate the robustness and self-assembly capabilities of PX-based DNA triangles.

Main Methods:

• Formation of a four-stranded triangular DNA species using PX interactions.
• Characterization of the triangular species using nondenaturing gel electrophoresis.
• Atomic force microscopy (AFM) to visualize structures and assess self-assembly into arrays.

Main Results:

• Successfully synthesized a robust, four-stranded DNA triangle mediated by PX interactions.
• Demonstrated that partial triangles can be extended into complete, stable four-stranded molecules.
• Showcased the self-assembly of these triangles into linear arrays when combined with a specific three-domain molecule.

Conclusions:

• Paranemic exchange interactions provide a viable alternative to traditional base pairing for constructing complex DNA nanostructures.
• PX-mediated DNA triangles are stable and can be programmed for higher-order self-assembly.
• This work expands the toolkit for DNA nanotechnology, enabling new designs for nanoscale objects and lattices.