Programmable 2D-to-3D structural transformation of DNA nanostructures triggered by single-stranded RNA

Area of Science:

• Molecular Biology
• Nanotechnology
• Biochemistry

Background:

• Controllable DNA nanostructures are key for molecular devices.
• Traditional toehold-mediated strand displacement limits conformational changes in DNA systems.
• A new method is needed to regulate DNA nanostructure transformations without toeholds.

Purpose of the Study:

• To develop a novel method for assembling and transforming DNA nanostructures using RNA.
• To create a toehold-free strand displacement strategy for DNA nanostructure rearrangement.
• To establish a DNA nanostructure-based diagnostic system for detecting specific nucleic acids.

Main Methods:

• Assembled a 2D DNA triangle using two DNA strands.
• Utilized RNA strand displacement to induce transformation into a 3D RNA-DNA hybrid quadrilateral.
• Confirmed nanostructure formation and transformation via cryogenic-electron microscopy (cryo-EM) and mass spectrometry (MS).
• Developed a nucleic acid detection strategy using single-stranded RNA displacement-induced transformation (SDT) coupled with isothermal amplification.

Main Results:

• Successfully assembled a 2D DNA triangle with only two DNA strands.
• Demonstrated RNA-induced strand displacement to form a 3D RNA-DNA hybrid quadrilateral without a toehold.
• Validated nanostructure transformations using cryo-EM and MS.
• Achieved successful detection of human papillomavirus (HPV) in clinical samples using the SDT strategy.

Conclusions:

• RNA strand displacement offers a new approach for constructing transformable DNA nanostructures.
• This method enables toehold-free regulation of DNA nanostructure conformational changes.
• The developed SDT strategy provides a novel platform for molecular diagnostics and target-specific signal reporting.