DNA brick self-assembly with an off-lattice potential

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.

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Cited by in corpus (8)

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• Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers
• Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly
• Lattice models and Monte Carlo methods for simulating DNA origami self-assembly
• Investigating the role of boundary bricks in DNA brick self-assembly
• Dissipative self-assembly of patchy particles under nonequilibrium drive: a computational study
• Building up DNA, bit by bit: a simple description of chain assembly