DNA brick self-assembly with an off-lattice potential

TL;DR

This paper presents Monte Carlo simulations of an off-lattice DNA brick model, demonstrating robust self-assembly into target structures and relating model parameters to DNA binding free energies.

Contribution

It introduces an off-lattice patchy-particle model for DNA bricks and explores its self-assembly behavior compared to previous lattice models.

Findings

Off-lattice model reproduces key behaviors of lattice models.

Relaxation of geometric constraints increases error-proneness.

Robust self-assembly into various structures observed.

Abstract

We report Monte Carlo simulations of a simple off-lattice patchy-particle model for DNA `bricks'. We relate the parameters that characterise this model with the binding free energy of pairs of single-stranded DNA molecules. We verify that an off-lattice potential parameterised in this way reproduces much of the behaviour seen with a simpler lattice model we introduced previously, although the relaxation of the geometric constraints leads to a more error-prone self-assembly pathway. We investigate the self-assembly process as a function of the strength of the non-specific interactions. We show that our off-lattice model for DNA bricks results in robust self-assembly into a variety of target structures.