The self-assembly of DNA Holliday junctions studied with a minimal model

TL;DR

This study uses a minimal coarse-grained DNA model to simulate the self-assembly of DNA nanostructures, revealing optimal temperature conditions and hierarchical assembly mechanisms for correct formation.

Contribution

Introduces a simple coarse-grained DNA model capable of simulating self-assembly and melting behaviors of DNA nanostructures, including Holliday junctions.

Findings

Assembly occurs best below target melting temperature and above misbonded aggregates.

Hierarchical assembly reduces misbonding in Holliday junctions.

Model accurately reproduces melting temperatures and allows strand displacement.

Abstract

In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to the phosphate-sugar backbone and the base. Using this model, we are able to simulate the self-assembly of both DNA duplexes and Holliday junctions from single-stranded DNA. We find that assembly is most successful in the temperature window below the melting temperatures of the target structure and above the melting temperature of misbonded aggregates. Furthermore, in the case of the Holliday junction, we show how a hierarchical assembly mechanism reduces the possibility of becoming trapped in misbonded configurations. The model is also able to reproduce the relative melting temperatures of different structures accurately, and allows strand displacement to occur.