Hybrid RNA/DNA Concatemers and Self-Limited Complexes: Structure and Prospects for Therapeutic Applications

Area of Science:

• Biochemistry
• Nanotechnology
• Molecular Biology

Background:

• Designing complex nucleic acid (NA) structures is crucial for advancements in biomedicine and NA nanotechnology.
• Developing convenient tools for predicting and controlling the assembly of multicomponent NA complexes remains a challenge.

Purpose of the Study:

• To analyze the formation of hybrid RNA/DNA concatemers and self-limited complexes using various oligonucleotide designs.
• To systematize the effects of linker size on the shape and subunit number of RNA/DNA, DNA/DNA, and RNA/RNA assemblies.
• To establish general rules for designing and transforming the geometry of NA complexes.

Main Methods:

• UV melting analysis
• Circular dichroism (CD) spectroscopy to confirm the A-form double helix of RNA/DNA complexes
• Gel shift assay to study complex formation

Main Results:

• Heat maps were generated to categorize complex types, serving as a design tool for NA constructs.
• General rules were identified for RNA/DNA, DNA/DNA, and RNA/RNA complexes, enabling predictable design and geometric transformation.
• Efficient degradation of RNA in hybrid self-limited complexes was demonstrated using RNase H and imidazole.

Conclusions:

• The developed heat maps and design rules provide a convenient method for creating diverse NA complexes.
• The findings facilitate the purposeful design and modification of NA complex geometry for specific applications.
• This research opens new avenues for supramolecular complex design in nanotechnology, nanomachinery, and biomedical fields.