Coarse-Grained Nucleic Acid-Protein Model for Hybrid Nanotechnology

TL;DR

This paper introduces a coarse-grained DNA-protein model to facilitate the design and simulation of hybrid nanostructures, combining DNA nanotechnology with protein interactions for materials and biological studies.

Contribution

The authors develop a novel coarse-grained model extending oxDNA/oxRNA to include proteins, enabling efficient simulation of hybrid DNA-protein nanostructures.

Findings

Successfully simulated DNA-protein nanocage

Modeled DNA wrapped around histones

Simulated nascent RNA in polymerase

Abstract

The emerging field of hybrid DNA - protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with versatility of protein interactions. However, the design and computational study of these hybrid structures is difficult due to the system sizes involved. To aid in the design and in silico analysis process, we introduce here a coarse-grained DNA/RNA-protein model that extends the oxDNA/oxRNA models of DNA/RNA with a coarse-grained model of proteins based on an anisotropic network model representation. Fully equipped with analysis scripts and visualization, our model aims to facilitate hybrid nanomaterial design towards eventual experimental realization, as well as enabling study of biological complexes. We further demonstrate its usage by simulating DNA-protein nanocage, DNA wrapped around histones, and a nascent RNA in polymerase.