DNA brick self-assembly with an off-lattice potential.

Area of Science:

• * Nanotechnology
• * Biophysics
• * Computational Chemistry

Background:

• * DNA nanotechnology utilizes DNA molecules for constructing nanoscale materials.
• * Previous lattice models simplified DNA brick self-assembly, but lacked geometric realism.
• * Understanding binding energies is crucial for predicting DNA self-assembly outcomes.

Purpose of the Study:

• * To develop and validate an off-lattice model for DNA brick self-assembly.
• * To correlate model parameters with single-stranded DNA binding free energies.
• * To investigate the influence of non-specific interactions on self-assembly fidelity.

Main Methods:

• * Monte Carlo simulations were performed on an off-lattice patchy-particle model.
• * Model parameters were calibrated using binding free energy data for DNA pairs.
• * The model's predictions were compared against a previously established lattice model.

Main Results:

• * The off-lattice model successfully reproduced key behaviors of the lattice model.
• * Geometric constraint relaxation in the off-lattice model increased self-assembly errors.
• * Self-assembly robustness was confirmed across various target structures.
• * Non-specific interaction strength was identified as a critical factor in assembly fidelity.

Conclusions:

• * The off-lattice model provides a more realistic simulation of DNA brick self-assembly.
• * The model accurately captures DNA binding thermodynamics.
• * This approach enables the design of complex DNA nanostructures with improved predictability.