Folding Competition and Dynamic Transformation in DNA Origami: Parallel Versus Antiparallel Crossovers

Area of Science:

• Nanotechnology
• Biomaterials Science
• Molecular Biology

Background:

• DNA origami is a powerful technique for creating nanostructures.
• Antiparallel crossovers are traditionally used, but parallel crossovers offer unique advantages.
• Parallel crossovers can enhance nuclease resistance and enable single-strand routing.

Purpose of the Study:

• To design and investigate DNA origami nanostructures utilizing parallel crossovers.
• To compare the folding behavior and properties of antiparallel and parallel DNA origami designs.
• To demonstrate dynamic transformations between antiparallel and parallel configurations.

Main Methods:

• Systematic design and synthesis of DNA origami nanostructures with varying antiparallel and parallel crossover arrangements.
• Competitive folding tests to assess design preference and folding pathways.
• Nuclease resistance assays and isothermal transformation studies using toehold-mediated displacement.

Main Results:

• The arrangement of staples near the central scaffold crossover dictates the shift between parallel and antiparallel conformations.
• 36 pairs of antiparallel and parallel designs were tested, with 12 designs ranked based on performance.
• A two-way isothermal transformation between antiparallel and parallel origami was achieved via toehold-mediated displacement.

Conclusions:

• Parallel DNA origami crossovers are crucial for developing dynamic nanodevices.
• The findings provide insights into the dynamics of antiparallel and parallel DNA origami.
• This research opens avenues for designing novel nanodevices, particularly for temperature-sensitive environments.