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Issue 13, 2021
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Coarse-grained nucleic acid–protein model for hybrid nanotechnology

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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 the 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.

Graphical abstract: Coarse-grained nucleic acid–protein model for hybrid nanotechnology

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Supplementary files

Article information


Submitted
12 Sep 2020
Accepted
16 Dec 2020
First published
16 Dec 2020

Soft Matter, 2021,17, 3586-3593
Article type
Paper

Coarse-grained nucleic acid–protein model for hybrid nanotechnology

J. Procyk, E. Poppleton and P. Šulc, Soft Matter, 2021, 17, 3586 DOI: 10.1039/D0SM01639J

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