Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation

Area of Science:

• Nanotechnology
• Polymer Science
• Molecular Biology

Background:

• Biological self-assembly creates complex nanoscale structures.
• Controlling self-assembly for nanotechnology requires encoding global architectures in small subunits.
• Strain accumulation via geometric frustration explains some self-assembly phenomena post-hoc.

Purpose of the Study:

• To utilize strain accumulation as a rational design principle for controlling self-assembling polymer length distributions.
• To engineer molecular subunits (PolyBricks) that perturb shape based on local interactions.
• To achieve predictable polymer lengths and reduce length uncertainty in self-assembled structures.

Main Methods:

• Design and synthesis of PolyBrick subunits using the DNA origami method.
• Investigating shape perturbations due to flexible allosteric blocking domains.
• Employing coarse-grained molecular dynamics and Monte Carlo simulations to analyze forces.

Main Results:

• PolyBricks enable polymers to approach Gaussian length distributions, with variance determined by strain free energy.
• Strain accumulation provides a mechanism to control polymer length distributions, moving beyond geometric distributions.
• Demonstrated that intersubunit binding and strain free energy are key thermodynamic factors for length control.
• Showed potential for tighter length distributions and uniform polymer lengths with increased subunit affinity.

Conclusions:

• Strain accumulation is a viable rational design principle for controlling molecular self-assembly.
• PolyBricks offer a method to engineer polymers with predictable lengths and reduced variability.
• This work advances the fundamental understanding of using mechanical stress in nanoscale self-assembly for targeted applications.