A simple screening strategy for complex RNA-DNA hybrid nanoshapes

Area of Science:

• Biotechnology and Nanotechnology
• Nucleic Acid Chemistry
• Materials Science

Background:

• Hybrid nucleic acid nanomaterials combine RNA and DNA for distinct architectural and functional roles.
• Designing stable RNA-DNA nanoshapes requires careful selection of compatible building blocks.
• Existing methods for identifying optimal RNA-DNA combinations can be complex.

Purpose of the Study:

• To develop a simple and robust screening strategy for identifying optimal RNA and DNA modules for hybrid nanoshapes.
• To demonstrate the preparation of polygonal RNA-DNA hybrid nanoshapes using the developed screening method.
• To showcase the versatility of the method with different RNA architectural joints.

Main Methods:

• Utilized gel electrophoresis under native folding conditions for screening nucleic acid module combinations.
• Employed a library of DNA connectors to identify optimal partners for RNA architectural joints.
• Focused on RNA-DNA hybrid nanoshapes incorporating internal loop motifs and three-way junction (3WJ) folds.

Main Results:

• Successfully identified optimal RNA-DNA module combinations that self-assemble into stable polygonal hybrid nanoshapes.
• Demonstrated the efficacy of the screening strategy through the preparation of specific RNA-DNA nanoshapes.
• Validated the selection process for identifying suitable DNA connectors for diverse RNA joints.

Conclusions:

• The developed gel electrophoresis screening strategy is a general and robust method for identifying and preparing RNA-DNA hybrid nanoshapes.
• This approach facilitates the creation of diverse nanostructures from discrete nucleic acid building blocks.
• The method simplifies the design and assembly of complex hybrid nucleic acid nanomaterials.