Insights into DNA-mediated interparticle interactions from a coarse-grained model

TL;DR

This paper introduces a detailed coarse-grained DNA model for simulating particle interactions, capturing key DNA behaviors to better understand self-assembly and kinetic barriers in DNA-functionalized particle systems.

Contribution

A new coarse-grained model of DNA-functionalized particles that explicitly represents DNA at the nucleotide level and includes specific DNA interactions, improving upon previous models.

Findings

Calculated free energies match experimental DNA-mediated interactions.

Model captures DNA hairpin and duplex formation.

Interaction dependence on DNA density, length, and temperature.

Abstract

DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA- functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions.