A computational framework for designing micron-scale crisscross DNA megastructures

Area of Science:

• Biotechnology
• Nanotechnology
• Synthetic Biology

Background:

• DNA origami enables precise nanoscale assembly of complex structures.
• Designing large DNA origami megastructures is challenging due to handle sequence assignment and parasitic interactions.
• Fabricating numerous unique DNA origami slats poses a significant logistical hurdle.

Purpose of the Study:

• To develop a unified framework for standardizing the design and fabrication of crisscross DNA origami megastructures.
• To address the challenges of handle sequence optimization and minimize parasitic binding.
• To enhance the accessibility and streamline laboratory workflows for DNA origami construction.

Main Methods:

• Utilized an evolutionary algorithm for optimizing handle sequence assignment.
• Developed an expanded handle library to increase design possibilities.
• Integrated algorithms into #-CAD, an open-source graphical application.

Main Results:

• Successfully designed and assembled large, multi-layered DNA origami megastructures with nanoscale precision.
• Minimized parasitic interactions between DNA origami slats, improving assembly yields.
• Demonstrated the framework's ability to produce structures previously at negligible yields.

Conclusions:

• The #-CAD framework standardizes and simplifies the design and fabrication of complex DNA origami megastructures.
• The integrated evolutionary algorithm and expanded handle library overcome key design and assembly challenges.
• This open-source application significantly enhances the accessibility of advanced DNA origami techniques for researchers.